This notebook is for performing downstream analysis of CYCLOPS. It includes running cosinor regression and assessing differential rhythmicity (two ways for both), calling the enrichR API via python, using fgsea in R, running PSEA, outputing files for making KEGG map diagrams, etc.

Load Packages

This notebook makes use of python via anaconda. Please make sure you install anaconda to proceed:

conda_list()

Select your conda environment of choice, in my case, item 2 from list above:

conda_list()[[2]][2] %>% 
  use_condaenv(required = TRUE)
print(paste("Using cond env:",conda_list()[[1]][2] ))
[1] "Using cond env: base"

Setup

Select the CYCLOPS ordering path and path to data file and path to DEseq2 differential expression results:

#path to cyclops ordering
path_to_cyclops_ordering = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/"

#path to normalized counts
path_to_tmm_file = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/tmms/scROSMAP/cogdx_controls/EdgeR_filt_normed/ExcSubtypes3and5_FiltByExprDefault_TMM.csv"

# optional path to file containing differential expression results
deseq_de_filename = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/simple_differential_expr/Exc3_5/Exc3_5_filtByExpr_combatSeq_edgeR_DE_exactTest.csv"

path_to_rosmap_clin = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Meta_data/cleaned_rosmap_meta_cogdxConds.csv"
metabolon_filename = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Metabolon/ROSMAP_Metabolon_HD4_Brain514_assay_data.csv"
metabolon_datakey = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Metabolon/ROSMAP_Metabolon_HD4_Data_Dictionary.csv"

#BHQ corrected p cutoff to be considered cycling in analysis:
isCyclingBHQCutoff = 0.1
percentile = 0.025
useBatch = T

Cosinor Regression and Differential Rhythmicity

Run cosinor regression and differential rhythmicity analysis with custom script and with compareRhythms library. I make use of Ensembl and Entrez IDs so I need the following translation dictionaries:

# read in translation dict between gene symbols and other alias
Ensembl_dict = readxl::read_xlsx("scROSMAP_ENSEMBL_dict.xlsx")

#run custom cycling and differential rhythmicity analysis
print("***Running cosinor and differential rhythms analysis***")
[1] "***Running cosinor and differential rhythms analysis***"
run_cycling_and_dr_analysis(path_to_cyclops_ordering, path_to_tmm_file, isCyclingSigCutoff = isCyclingBHQCutoff, percentile = percentile, useBatch = useBatch)

Running is_cycling() on cond_subset: cond_0
NOTE: Using batches in regression.

[>-------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>-----------------------------------------------------------------------------------------------------------------------------------------]   2%
[===>----------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   5%
[======>-------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>----------------------------------------------------------------------------------------------------------------------------------]   7%
[==========>---------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]  10%
[=============>------------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  12%
[================>---------------------------------------------------------------------------------------------------------------------------]  12%
[=================>--------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  15%
[====================>-----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  17%
[=======================>--------------------------------------------------------------------------------------------------------------------]  17%
[========================>-------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  20%
[===========================>----------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  22%
[==============================>-------------------------------------------------------------------------------------------------------------]  22%
[===============================>------------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  25%
[==================================>---------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  27%
[=====================================>------------------------------------------------------------------------------------------------------]  27%
[======================================>-----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  30%
[=========================================>--------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  32%
[============================================>-----------------------------------------------------------------------------------------------]  32%
[=============================================>----------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  35%
[================================================>-------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  37%
[===================================================>----------------------------------------------------------------------------------------]  37%
[====================================================>---------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  40%
[=======================================================>------------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  42%
[==========================================================>---------------------------------------------------------------------------------]  42%
[===========================================================>--------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  45%
[==============================================================>-----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  47%
[=================================================================>--------------------------------------------------------------------------]  47%
[==================================================================>-------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  50%
[=====================================================================>----------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  52%
[========================================================================>-------------------------------------------------------------------]  52%
[=========================================================================>------------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  55%
[============================================================================>---------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  57%
[===============================================================================>------------------------------------------------------------]  57%
[================================================================================>-----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  60%
[===================================================================================>--------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  62%
[======================================================================================>-----------------------------------------------------]  62%
[=======================================================================================>----------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  65%
[==========================================================================================>-------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  67%
[=============================================================================================>----------------------------------------------]  67%
[==============================================================================================>---------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  70%
[=================================================================================================>------------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  72%
[====================================================================================================>---------------------------------------]  72%
[=====================================================================================================>--------------------------------------]  73%
[======================================================================================================>-------------------------------------]  73%
[======================================================================================================>-------------------------------------]  74%
[=======================================================================================================>------------------------------------]  74%
[=======================================================================================================>------------------------------------]  75%
[========================================================================================================>-----------------------------------]  75%
[=========================================================================================================>----------------------------------]  75%
[=========================================================================================================>----------------------------------]  76%
[==========================================================================================================>---------------------------------]  76%
[==========================================================================================================>---------------------------------]  77%
[===========================================================================================================>--------------------------------]  77%
[============================================================================================================>-------------------------------]  78%
[=============================================================================================================>------------------------------]  78%
[=============================================================================================================>------------------------------]  79%
[==============================================================================================================>-----------------------------]  79%
[==============================================================================================================>-----------------------------]  80%
[===============================================================================================================>----------------------------]  80%
[================================================================================================================>---------------------------]  80%
[================================================================================================================>---------------------------]  81%
[=================================================================================================================>--------------------------]  81%
[=================================================================================================================>--------------------------]  82%
[==================================================================================================================>-------------------------]  82%
[===================================================================================================================>------------------------]  83%
[====================================================================================================================>-----------------------]  83%
[====================================================================================================================>-----------------------]  84%
[=====================================================================================================================>----------------------]  84%
[=====================================================================================================================>----------------------]  85%
[======================================================================================================================>---------------------]  85%
[=======================================================================================================================>--------------------]  85%
[=======================================================================================================================>--------------------]  86%
[========================================================================================================================>-------------------]  86%
[========================================================================================================================>-------------------]  87%
[=========================================================================================================================>------------------]  87%
[==========================================================================================================================>-----------------]  88%
[===========================================================================================================================>----------------]  88%
[===========================================================================================================================>----------------]  89%
[============================================================================================================================>---------------]  89%
[============================================================================================================================>---------------]  90%
[=============================================================================================================================>--------------]  90%
[==============================================================================================================================>-------------]  90%
[==============================================================================================================================>-------------]  91%
[===============================================================================================================================>------------]  91%
[===============================================================================================================================>------------]  92%
[================================================================================================================================>-----------]  92%
[=================================================================================================================================>----------]  93%
[==================================================================================================================================>---------]  93%
[==================================================================================================================================>---------]  94%
[===================================================================================================================================>--------]  94%
[===================================================================================================================================>--------]  95%
[====================================================================================================================================>-------]  95%
[=====================================================================================================================================>------]  95%
[=====================================================================================================================================>------]  96%
[======================================================================================================================================>-----]  96%
[======================================================================================================================================>-----]  97%
[=======================================================================================================================================>----]  97%
[========================================================================================================================================>---]  98%
[=========================================================================================================================================>--]  98%
[=========================================================================================================================================>--]  99%
[==========================================================================================================================================>-]  99%
[==========================================================================================================================================>-] 100%
[===========================================================================================================================================>] 100%

Running is_cycling() on cond_subset: cond_1
NOTE: Using batches in regression.

[>-------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>-----------------------------------------------------------------------------------------------------------------------------------------]   2%
[===>----------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   5%
[======>-------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>----------------------------------------------------------------------------------------------------------------------------------]   7%
[==========>---------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]  10%
[=============>------------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  12%
[================>---------------------------------------------------------------------------------------------------------------------------]  12%
[=================>--------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  15%
[====================>-----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  17%
[=======================>--------------------------------------------------------------------------------------------------------------------]  17%
[========================>-------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  20%
[===========================>----------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  22%
[==============================>-------------------------------------------------------------------------------------------------------------]  22%
[===============================>------------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  25%
[==================================>---------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  27%
[=====================================>------------------------------------------------------------------------------------------------------]  27%
[======================================>-----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  30%
[=========================================>--------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  32%
[============================================>-----------------------------------------------------------------------------------------------]  32%
[=============================================>----------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  35%
[================================================>-------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  37%
[===================================================>----------------------------------------------------------------------------------------]  37%
[====================================================>---------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  40%
[=======================================================>------------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  42%
[==========================================================>---------------------------------------------------------------------------------]  42%
[===========================================================>--------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  45%
[==============================================================>-----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  47%
[=================================================================>--------------------------------------------------------------------------]  47%
[==================================================================>-------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  50%
[=====================================================================>----------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  52%
[========================================================================>-------------------------------------------------------------------]  52%
[=========================================================================>------------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  55%
[============================================================================>---------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  57%
[===============================================================================>------------------------------------------------------------]  57%
[================================================================================>-----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  60%
[===================================================================================>--------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  62%
[======================================================================================>-----------------------------------------------------]  62%
[=======================================================================================>----------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  65%
[==========================================================================================>-------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  67%
[=============================================================================================>----------------------------------------------]  67%
[==============================================================================================>---------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  70%
[=================================================================================================>------------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  72%
[====================================================================================================>---------------------------------------]  72%
[=====================================================================================================>--------------------------------------]  73%
[======================================================================================================>-------------------------------------]  73%
[======================================================================================================>-------------------------------------]  74%
[=======================================================================================================>------------------------------------]  74%
[=======================================================================================================>------------------------------------]  75%
[========================================================================================================>-----------------------------------]  75%
[=========================================================================================================>----------------------------------]  75%
[=========================================================================================================>----------------------------------]  76%
[==========================================================================================================>---------------------------------]  76%
[==========================================================================================================>---------------------------------]  77%
[===========================================================================================================>--------------------------------]  77%
[============================================================================================================>-------------------------------]  78%
[=============================================================================================================>------------------------------]  78%
[=============================================================================================================>------------------------------]  79%
[==============================================================================================================>-----------------------------]  79%
[==============================================================================================================>-----------------------------]  80%
[===============================================================================================================>----------------------------]  80%
[================================================================================================================>---------------------------]  80%
[================================================================================================================>---------------------------]  81%
[=================================================================================================================>--------------------------]  81%
[=================================================================================================================>--------------------------]  82%
[==================================================================================================================>-------------------------]  82%
[===================================================================================================================>------------------------]  83%
[====================================================================================================================>-----------------------]  83%
[====================================================================================================================>-----------------------]  84%
[=====================================================================================================================>----------------------]  84%
[=====================================================================================================================>----------------------]  85%
[======================================================================================================================>---------------------]  85%
[=======================================================================================================================>--------------------]  85%
[=======================================================================================================================>--------------------]  86%
[========================================================================================================================>-------------------]  86%
[========================================================================================================================>-------------------]  87%
[=========================================================================================================================>------------------]  87%
[==========================================================================================================================>-----------------]  88%
[===========================================================================================================================>----------------]  88%
[===========================================================================================================================>----------------]  89%
[============================================================================================================================>---------------]  89%
[============================================================================================================================>---------------]  90%
[=============================================================================================================================>--------------]  90%
[==============================================================================================================================>-------------]  90%
[==============================================================================================================================>-------------]  91%
[===============================================================================================================================>------------]  91%
[===============================================================================================================================>------------]  92%
[================================================================================================================================>-----------]  92%
[=================================================================================================================================>----------]  93%
[==================================================================================================================================>---------]  93%
[==================================================================================================================================>---------]  94%
[===================================================================================================================================>--------]  94%
[===================================================================================================================================>--------]  95%
[====================================================================================================================================>-------]  95%
[=====================================================================================================================================>------]  95%
[=====================================================================================================================================>------]  96%
[======================================================================================================================================>-----]  96%
[======================================================================================================================================>-----]  97%
[=======================================================================================================================================>----]  97%
[========================================================================================================================================>---]  98%
[=========================================================================================================================================>--]  98%
[=========================================================================================================================================>--]  99%
[==========================================================================================================================================>-]  99%
[==========================================================================================================================================>-] 100%
[===========================================================================================================================================>] 100%

Running is_cycling_method2() (analogue of compareRhythms) on all subjects
NOTE: Using batches in regression.

[--------------------------------------------------------------------------------------------------------------------------------------------]   0%
[>-------------------------------------------------------------------------------------------------------------------------------------------]   0%
[>-------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>-----------------------------------------------------------------------------------------------------------------------------------------]   2%
[===>----------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   5%
[======>-------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>----------------------------------------------------------------------------------------------------------------------------------]   7%
[==========>---------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]  10%
[=============>------------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  12%
[================>---------------------------------------------------------------------------------------------------------------------------]  12%
[=================>--------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  15%
[====================>-----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  17%
[=======================>--------------------------------------------------------------------------------------------------------------------]  17%
[========================>-------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  20%
[===========================>----------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  22%
[==============================>-------------------------------------------------------------------------------------------------------------]  22%
[===============================>------------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  25%
[==================================>---------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  27%
[=====================================>------------------------------------------------------------------------------------------------------]  27%
[======================================>-----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  30%
[=========================================>--------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  32%
[============================================>-----------------------------------------------------------------------------------------------]  32%
[=============================================>----------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  35%
[================================================>-------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  37%
[===================================================>----------------------------------------------------------------------------------------]  37%
[====================================================>---------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  40%
[=======================================================>------------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  42%
[==========================================================>---------------------------------------------------------------------------------]  42%
[===========================================================>--------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  45%
[==============================================================>-----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  47%
[=================================================================>--------------------------------------------------------------------------]  47%
[==================================================================>-------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  50%
[=====================================================================>----------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  52%
[========================================================================>-------------------------------------------------------------------]  52%
[=========================================================================>------------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  55%
[============================================================================>---------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  57%
[===============================================================================>------------------------------------------------------------]  57%
[================================================================================>-----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  60%
[===================================================================================>--------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  62%
[======================================================================================>-----------------------------------------------------]  62%
[=======================================================================================>----------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  65%
[==========================================================================================>-------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  67%
[=============================================================================================>----------------------------------------------]  67%
[==============================================================================================>---------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  70%
[=================================================================================================>------------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  72%
[====================================================================================================>---------------------------------------]  72%
[=====================================================================================================>--------------------------------------]  73%
[======================================================================================================>-------------------------------------]  73%
[======================================================================================================>-------------------------------------]  74%
[=======================================================================================================>------------------------------------]  74%
[=======================================================================================================>------------------------------------]  75%
[========================================================================================================>-----------------------------------]  75%
[=========================================================================================================>----------------------------------]  75%
[=========================================================================================================>----------------------------------]  76%
[==========================================================================================================>---------------------------------]  76%
[==========================================================================================================>---------------------------------]  77%
[===========================================================================================================>--------------------------------]  77%
[============================================================================================================>-------------------------------]  78%
[=============================================================================================================>------------------------------]  78%
[=============================================================================================================>------------------------------]  79%
[==============================================================================================================>-----------------------------]  79%
[==============================================================================================================>-----------------------------]  80%
[===============================================================================================================>----------------------------]  80%
[================================================================================================================>---------------------------]  80%
[================================================================================================================>---------------------------]  81%
[=================================================================================================================>--------------------------]  81%
[=================================================================================================================>--------------------------]  82%
[==================================================================================================================>-------------------------]  82%
[===================================================================================================================>------------------------]  83%
[====================================================================================================================>-----------------------]  83%
[====================================================================================================================>-----------------------]  84%
[=====================================================================================================================>----------------------]  84%
[=====================================================================================================================>----------------------]  85%
[======================================================================================================================>---------------------]  85%
[=======================================================================================================================>--------------------]  85%
[=======================================================================================================================>--------------------]  86%
[========================================================================================================================>-------------------]  86%
[========================================================================================================================>-------------------]  87%
[=========================================================================================================================>------------------]  87%
[==========================================================================================================================>-----------------]  88%
[===========================================================================================================================>----------------]  88%
[===========================================================================================================================>----------------]  89%
[============================================================================================================================>---------------]  89%
[============================================================================================================================>---------------]  90%
[=============================================================================================================================>--------------]  90%
[==============================================================================================================================>-------------]  90%
[==============================================================================================================================>-------------]  91%
[===============================================================================================================================>------------]  91%
[===============================================================================================================================>------------]  92%
[================================================================================================================================>-----------]  92%
[=================================================================================================================================>----------]  93%
[==================================================================================================================================>---------]  93%
[==================================================================================================================================>---------]  94%
[===================================================================================================================================>--------]  94%
[===================================================================================================================================>--------]  95%
[====================================================================================================================================>-------]  95%
[=====================================================================================================================================>------]  95%
[=====================================================================================================================================>------]  96%
[======================================================================================================================================>-----]  96%
[======================================================================================================================================>-----]  97%
[=======================================================================================================================================>----]  97%
[========================================================================================================================================>---]  98%
[=========================================================================================================================================>--]  98%
[=========================================================================================================================================>--]  99%
[==========================================================================================================================================>-]  99%
[==========================================================================================================================================>-] 100%
[===========================================================================================================================================>] 100%

Running Mesor_differences()
NOTE: Using batches in regression.

[--------------------------------------------------------------------------------------------------------------------------------------------]   0%
[>-------------------------------------------------------------------------------------------------------------------------------------------]   0%
[>-------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>-----------------------------------------------------------------------------------------------------------------------------------------]   2%
[===>----------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   5%
[======>-------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>----------------------------------------------------------------------------------------------------------------------------------]   7%
[==========>---------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]  10%
[=============>------------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  12%
[================>---------------------------------------------------------------------------------------------------------------------------]  12%
[=================>--------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  15%
[====================>-----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  17%
[=======================>--------------------------------------------------------------------------------------------------------------------]  17%
[========================>-------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  20%
[===========================>----------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  22%
[==============================>-------------------------------------------------------------------------------------------------------------]  22%
[===============================>------------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  25%
[==================================>---------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  27%
[=====================================>------------------------------------------------------------------------------------------------------]  27%
[======================================>-----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  30%
[=========================================>--------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  32%
[============================================>-----------------------------------------------------------------------------------------------]  32%
[=============================================>----------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  35%
[================================================>-------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  37%
[===================================================>----------------------------------------------------------------------------------------]  37%
[====================================================>---------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  40%
[=======================================================>------------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  42%
[==========================================================>---------------------------------------------------------------------------------]  42%
[===========================================================>--------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  45%
[==============================================================>-----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  47%
[=================================================================>--------------------------------------------------------------------------]  47%
[==================================================================>-------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  50%
[=====================================================================>----------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  52%
[========================================================================>-------------------------------------------------------------------]  52%
[=========================================================================>------------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  55%
[============================================================================>---------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  57%
[===============================================================================>------------------------------------------------------------]  57%
[================================================================================>-----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  60%
[===================================================================================>--------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  62%
[======================================================================================>-----------------------------------------------------]  62%
[=======================================================================================>----------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  65%
[==========================================================================================>-------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  67%
[=============================================================================================>----------------------------------------------]  67%
[==============================================================================================>---------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  70%
[=================================================================================================>------------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  72%
[====================================================================================================>---------------------------------------]  72%
[=====================================================================================================>--------------------------------------]  73%
[======================================================================================================>-------------------------------------]  73%
[======================================================================================================>-------------------------------------]  74%
[=======================================================================================================>------------------------------------]  74%
[=======================================================================================================>------------------------------------]  75%
[========================================================================================================>-----------------------------------]  75%
[=========================================================================================================>----------------------------------]  75%
[=========================================================================================================>----------------------------------]  76%
[==========================================================================================================>---------------------------------]  76%
[==========================================================================================================>---------------------------------]  77%
[===========================================================================================================>--------------------------------]  77%
[============================================================================================================>-------------------------------]  78%
[=============================================================================================================>------------------------------]  78%
[=============================================================================================================>------------------------------]  79%
[==============================================================================================================>-----------------------------]  79%
[==============================================================================================================>-----------------------------]  80%
[===============================================================================================================>----------------------------]  80%
[================================================================================================================>---------------------------]  80%
[================================================================================================================>---------------------------]  81%
[=================================================================================================================>--------------------------]  81%
[=================================================================================================================>--------------------------]  82%
[==================================================================================================================>-------------------------]  82%
[===================================================================================================================>------------------------]  83%
[====================================================================================================================>-----------------------]  83%
[====================================================================================================================>-----------------------]  84%
[=====================================================================================================================>----------------------]  84%
[=====================================================================================================================>----------------------]  85%
[======================================================================================================================>---------------------]  85%
[=======================================================================================================================>--------------------]  85%
[=======================================================================================================================>--------------------]  86%
[========================================================================================================================>-------------------]  86%
[========================================================================================================================>-------------------]  87%
[=========================================================================================================================>------------------]  87%
[==========================================================================================================================>-----------------]  88%
[===========================================================================================================================>----------------]  88%
[===========================================================================================================================>----------------]  89%
[============================================================================================================================>---------------]  89%
[============================================================================================================================>---------------]  90%
[=============================================================================================================================>--------------]  90%
[==============================================================================================================================>-------------]  90%
[==============================================================================================================================>-------------]  91%
[===============================================================================================================================>------------]  91%
[===============================================================================================================================>------------]  92%
[================================================================================================================================>-----------]  92%
[=================================================================================================================================>----------]  93%
[==================================================================================================================================>---------]  93%
[==================================================================================================================================>---------]  94%
[===================================================================================================================================>--------]  94%
[===================================================================================================================================>--------]  95%
[====================================================================================================================================>-------]  95%
[=====================================================================================================================================>------]  95%
[=====================================================================================================================================>------]  96%
[======================================================================================================================================>-----]  96%
[======================================================================================================================================>-----]  97%
[=======================================================================================================================================>----]  97%
[========================================================================================================================================>---]  98%
[=========================================================================================================================================>--]  98%
[=========================================================================================================================================>--]  99%
[==========================================================================================================================================>-]  99%
[==========================================================================================================================================>-] 100%
[===========================================================================================================================================>] 100%
[============================================================================================================================================] 100%
                                                                                                                                                   

Running diff_rhyth_AD_severity()
NOTE: Using batches in regression.
Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Using compatibility `.name_repair`.

Running diff_rhyth() on seedlist of size: 2287
NOTE: Using batches in regression.

[==>-----------------------------------------------------------------------------------------------------------------------------------------]   2%
[===>----------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   5%
[======>-------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>----------------------------------------------------------------------------------------------------------------------------------]   7%
[==========>---------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]  10%
[=============>------------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  12%
[================>---------------------------------------------------------------------------------------------------------------------------]  12%
[=================>--------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  15%
[====================>-----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  17%
[=======================>--------------------------------------------------------------------------------------------------------------------]  17%
[========================>-------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  20%
[===========================>----------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  22%
[==============================>-------------------------------------------------------------------------------------------------------------]  22%
[===============================>------------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  25%
[==================================>---------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  27%
[=====================================>------------------------------------------------------------------------------------------------------]  27%
[======================================>-----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  30%
[=========================================>--------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  32%
[============================================>-----------------------------------------------------------------------------------------------]  32%
[=============================================>----------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  35%
[================================================>-------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  37%
[===================================================>----------------------------------------------------------------------------------------]  37%
[====================================================>---------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  40%
[=======================================================>------------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  42%
[==========================================================>---------------------------------------------------------------------------------]  42%
[===========================================================>--------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  45%
[==============================================================>-----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  47%
[=================================================================>--------------------------------------------------------------------------]  47%
[==================================================================>-------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  50%
[=====================================================================>----------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  52%
[========================================================================>-------------------------------------------------------------------]  52%
[=========================================================================>------------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  55%
[============================================================================>---------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  57%
[===============================================================================>------------------------------------------------------------]  57%
[================================================================================>-----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  60%
[===================================================================================>--------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  62%
[======================================================================================>-----------------------------------------------------]  62%
[=======================================================================================>----------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  65%
[==========================================================================================>-------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  67%
[=============================================================================================>----------------------------------------------]  67%
[==============================================================================================>---------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  70%
[=================================================================================================>------------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  72%
[====================================================================================================>---------------------------------------]  72%
[=====================================================================================================>--------------------------------------]  73%
[======================================================================================================>-------------------------------------]  73%
[======================================================================================================>-------------------------------------]  74%
[=======================================================================================================>------------------------------------]  74%
[=======================================================================================================>------------------------------------]  75%
[========================================================================================================>-----------------------------------]  75%
[=========================================================================================================>----------------------------------]  75%
[=========================================================================================================>----------------------------------]  76%
[==========================================================================================================>---------------------------------]  76%
[==========================================================================================================>---------------------------------]  77%
[===========================================================================================================>--------------------------------]  77%
[============================================================================================================>-------------------------------]  78%
[=============================================================================================================>------------------------------]  78%
[=============================================================================================================>------------------------------]  79%
[==============================================================================================================>-----------------------------]  79%
[==============================================================================================================>-----------------------------]  80%
[===============================================================================================================>----------------------------]  80%
[================================================================================================================>---------------------------]  80%
[================================================================================================================>---------------------------]  81%
[=================================================================================================================>--------------------------]  81%
[=================================================================================================================>--------------------------]  82%
[==================================================================================================================>-------------------------]  82%
[===================================================================================================================>------------------------]  83%
[====================================================================================================================>-----------------------]  83%
[====================================================================================================================>-----------------------]  84%
[=====================================================================================================================>----------------------]  84%
[=====================================================================================================================>----------------------]  85%
[======================================================================================================================>---------------------]  85%
[=======================================================================================================================>--------------------]  85%
[=======================================================================================================================>--------------------]  86%
[========================================================================================================================>-------------------]  86%
[========================================================================================================================>-------------------]  87%
[=========================================================================================================================>------------------]  87%
[==========================================================================================================================>-----------------]  88%
[===========================================================================================================================>----------------]  88%
[===========================================================================================================================>----------------]  89%
[============================================================================================================================>---------------]  89%
[============================================================================================================================>---------------]  90%
[=============================================================================================================================>--------------]  90%
[==============================================================================================================================>-------------]  90%
[==============================================================================================================================>-------------]  91%
[===============================================================================================================================>------------]  91%
[===============================================================================================================================>------------]  92%
[================================================================================================================================>-----------]  92%
[=================================================================================================================================>----------]  93%
[==================================================================================================================================>---------]  93%
[==================================================================================================================================>---------]  94%
[===================================================================================================================================>--------]  94%
[===================================================================================================================================>--------]  95%
[====================================================================================================================================>-------]  95%
[=====================================================================================================================================>------]  95%
[=====================================================================================================================================>------]  96%
[======================================================================================================================================>-----]  96%
[======================================================================================================================================>-----]  97%
[=======================================================================================================================================>----]  97%
[========================================================================================================================================>---]  98%
[=========================================================================================================================================>--]  98%
[=========================================================================================================================================>--]  99%
[==========================================================================================================================================>-]  99%
[==========================================================================================================================================>-] 100%
[===========================================================================================================================================>] 100%
[============================================================================================================================================] 100%
                                                                                                                                                   

Running diff_rhyth() on seedlist of size: 831
NOTE: Using batches in regression.

[=======>------------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>----------------------------------------------------------------------------------------------------------------------------------]   7%
[==========>---------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]  10%
[=============>------------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  12%
[================>---------------------------------------------------------------------------------------------------------------------------]  12%
[=================>--------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  15%
[====================>-----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  17%
[=======================>--------------------------------------------------------------------------------------------------------------------]  17%
[========================>-------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  20%
[===========================>----------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  22%
[==============================>-------------------------------------------------------------------------------------------------------------]  22%
[===============================>------------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  25%
[==================================>---------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  27%
[=====================================>------------------------------------------------------------------------------------------------------]  27%
[======================================>-----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  30%
[=========================================>--------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  32%
[============================================>-----------------------------------------------------------------------------------------------]  32%
[=============================================>----------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  35%
[================================================>-------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  37%
[===================================================>----------------------------------------------------------------------------------------]  37%
[====================================================>---------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  40%
[=======================================================>------------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  42%
[==========================================================>---------------------------------------------------------------------------------]  42%
[===========================================================>--------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  45%
[==============================================================>-----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  47%
[=================================================================>--------------------------------------------------------------------------]  47%
[==================================================================>-------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  50%
[=====================================================================>----------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  52%
[========================================================================>-------------------------------------------------------------------]  52%
[=========================================================================>------------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  55%
[============================================================================>---------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  57%
[===============================================================================>------------------------------------------------------------]  57%
[================================================================================>-----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  60%
[===================================================================================>--------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  62%
[======================================================================================>-----------------------------------------------------]  62%
[=======================================================================================>----------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  65%
[==========================================================================================>-------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  67%
[=============================================================================================>----------------------------------------------]  67%
[==============================================================================================>---------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  70%
[=================================================================================================>------------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  72%
[====================================================================================================>---------------------------------------]  72%
[=====================================================================================================>--------------------------------------]  73%
[======================================================================================================>-------------------------------------]  73%
[======================================================================================================>-------------------------------------]  74%
[=======================================================================================================>------------------------------------]  74%
[=======================================================================================================>------------------------------------]  75%
[========================================================================================================>-----------------------------------]  75%
[=========================================================================================================>----------------------------------]  75%
[=========================================================================================================>----------------------------------]  76%
[==========================================================================================================>---------------------------------]  76%
[==========================================================================================================>---------------------------------]  77%
[===========================================================================================================>--------------------------------]  77%
[============================================================================================================>-------------------------------]  78%
[=============================================================================================================>------------------------------]  78%
[=============================================================================================================>------------------------------]  79%
[==============================================================================================================>-----------------------------]  79%
[==============================================================================================================>-----------------------------]  80%
[===============================================================================================================>----------------------------]  80%
[================================================================================================================>---------------------------]  80%
[================================================================================================================>---------------------------]  81%
[=================================================================================================================>--------------------------]  81%
[=================================================================================================================>--------------------------]  82%
[==================================================================================================================>-------------------------]  82%
[===================================================================================================================>------------------------]  83%
[====================================================================================================================>-----------------------]  83%
[====================================================================================================================>-----------------------]  84%
[=====================================================================================================================>----------------------]  84%
[=====================================================================================================================>----------------------]  85%
[======================================================================================================================>---------------------]  85%
[=======================================================================================================================>--------------------]  85%
[=======================================================================================================================>--------------------]  86%
[========================================================================================================================>-------------------]  86%
[========================================================================================================================>-------------------]  87%
[=========================================================================================================================>------------------]  87%
[==========================================================================================================================>-----------------]  88%
[===========================================================================================================================>----------------]  88%
[===========================================================================================================================>----------------]  89%
[============================================================================================================================>---------------]  89%
[============================================================================================================================>---------------]  90%
[=============================================================================================================================>--------------]  90%
[==============================================================================================================================>-------------]  90%
[==============================================================================================================================>-------------]  91%
[===============================================================================================================================>------------]  91%
[===============================================================================================================================>------------]  92%
[================================================================================================================================>-----------]  92%
[=================================================================================================================================>----------]  93%
[==================================================================================================================================>---------]  93%
[==================================================================================================================================>---------]  94%
[===================================================================================================================================>--------]  94%
[===================================================================================================================================>--------]  95%
[====================================================================================================================================>-------]  95%
[=====================================================================================================================================>------]  95%
[=====================================================================================================================================>------]  96%
[======================================================================================================================================>-----]  96%
[======================================================================================================================================>-----]  97%
[=======================================================================================================================================>----]  97%
[========================================================================================================================================>---]  98%
[=========================================================================================================================================>--]  98%
[=========================================================================================================================================>--]  99%
[==========================================================================================================================================>-]  99%
[==========================================================================================================================================>-] 100%
[===========================================================================================================================================>] 100%
[============================================================================================================================================] 100%
                                                                                                                                                   

Running diff_rhyth() on seedlist of size: 10771
NOTE: Using batches in regression.

[>-------------------------------------------------------------------------------------------------------------------------------------------]   0%
[>-------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>-----------------------------------------------------------------------------------------------------------------------------------------]   2%
[===>----------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   5%
[======>-------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>----------------------------------------------------------------------------------------------------------------------------------]   7%
[==========>---------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]  10%
[=============>------------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  12%
[================>---------------------------------------------------------------------------------------------------------------------------]  12%
[=================>--------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  15%
[====================>-----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  17%
[=======================>--------------------------------------------------------------------------------------------------------------------]  17%
[========================>-------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  20%
[===========================>----------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  22%
[==============================>-------------------------------------------------------------------------------------------------------------]  22%
[===============================>------------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  25%
[==================================>---------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  27%
[=====================================>------------------------------------------------------------------------------------------------------]  27%
[======================================>-----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  30%
[=========================================>--------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  32%
[============================================>-----------------------------------------------------------------------------------------------]  32%
[=============================================>----------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  35%
[================================================>-------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  37%
[===================================================>----------------------------------------------------------------------------------------]  37%
[====================================================>---------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  40%
[=======================================================>------------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  42%
[==========================================================>---------------------------------------------------------------------------------]  42%
[===========================================================>--------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  45%
[==============================================================>-----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  47%
[=================================================================>--------------------------------------------------------------------------]  47%
[==================================================================>-------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  50%
[=====================================================================>----------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  52%
[========================================================================>-------------------------------------------------------------------]  52%
[=========================================================================>------------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  55%
[============================================================================>---------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  57%
[===============================================================================>------------------------------------------------------------]  57%
[================================================================================>-----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  60%
[===================================================================================>--------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  62%
[======================================================================================>-----------------------------------------------------]  62%
[=======================================================================================>----------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  65%
[==========================================================================================>-------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  67%
[=============================================================================================>----------------------------------------------]  67%
[==============================================================================================>---------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  70%
[=================================================================================================>------------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  72%
[====================================================================================================>---------------------------------------]  72%
[=====================================================================================================>--------------------------------------]  73%
[======================================================================================================>-------------------------------------]  73%
[======================================================================================================>-------------------------------------]  74%
[=======================================================================================================>------------------------------------]  74%
[=======================================================================================================>------------------------------------]  75%
[========================================================================================================>-----------------------------------]  75%
[=========================================================================================================>----------------------------------]  75%
[=========================================================================================================>----------------------------------]  76%
[==========================================================================================================>---------------------------------]  76%
[==========================================================================================================>---------------------------------]  77%
[===========================================================================================================>--------------------------------]  77%
[============================================================================================================>-------------------------------]  78%
[=============================================================================================================>------------------------------]  78%
[=============================================================================================================>------------------------------]  79%
[==============================================================================================================>-----------------------------]  79%
[==============================================================================================================>-----------------------------]  80%
[===============================================================================================================>----------------------------]  80%
[================================================================================================================>---------------------------]  80%
[================================================================================================================>---------------------------]  81%
[=================================================================================================================>--------------------------]  81%
[=================================================================================================================>--------------------------]  82%
[==================================================================================================================>-------------------------]  82%
[===================================================================================================================>------------------------]  83%
[====================================================================================================================>-----------------------]  83%
[====================================================================================================================>-----------------------]  84%
[=====================================================================================================================>----------------------]  84%
[=====================================================================================================================>----------------------]  85%
[======================================================================================================================>---------------------]  85%
[=======================================================================================================================>--------------------]  85%
[=======================================================================================================================>--------------------]  86%
[========================================================================================================================>-------------------]  86%
[========================================================================================================================>-------------------]  87%
[=========================================================================================================================>------------------]  87%
[==========================================================================================================================>-----------------]  88%
[===========================================================================================================================>----------------]  88%
[===========================================================================================================================>----------------]  89%
[============================================================================================================================>---------------]  89%
[============================================================================================================================>---------------]  90%
[=============================================================================================================================>--------------]  90%
[==============================================================================================================================>-------------]  90%
[==============================================================================================================================>-------------]  91%
[===============================================================================================================================>------------]  91%
[===============================================================================================================================>------------]  92%
[================================================================================================================================>-----------]  92%
[=================================================================================================================================>----------]  93%
[==================================================================================================================================>---------]  93%
[==================================================================================================================================>---------]  94%
[===================================================================================================================================>--------]  94%
[===================================================================================================================================>--------]  95%
[====================================================================================================================================>-------]  95%
[=====================================================================================================================================>------]  95%
[=====================================================================================================================================>------]  96%
[======================================================================================================================================>-----]  96%
[======================================================================================================================================>-----]  97%
[=======================================================================================================================================>----]  97%
[========================================================================================================================================>---]  98%
[=========================================================================================================================================>--]  98%
[=========================================================================================================================================>--]  99%
[==========================================================================================================================================>-]  99%
[==========================================================================================================================================>-] 100%
[===========================================================================================================================================>] 100%
[============================================================================================================================================] 100%
                                                                                                                                                   

Running diff_rhyth() on seedlist of size: 2300
NOTE: Using batches in regression.

[==>-----------------------------------------------------------------------------------------------------------------------------------------]   2%
[===>----------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   5%
[======>-------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>----------------------------------------------------------------------------------------------------------------------------------]   7%
[==========>---------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]  10%
[=============>------------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  12%
[================>---------------------------------------------------------------------------------------------------------------------------]  12%
[=================>--------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  15%
[====================>-----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  17%
[=======================>--------------------------------------------------------------------------------------------------------------------]  17%
[========================>-------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  20%
[===========================>----------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  22%
[==============================>-------------------------------------------------------------------------------------------------------------]  22%
[===============================>------------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  25%
[==================================>---------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  27%
[=====================================>------------------------------------------------------------------------------------------------------]  27%
[======================================>-----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  30%
[=========================================>--------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  32%
[============================================>-----------------------------------------------------------------------------------------------]  32%
[=============================================>----------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  35%
[================================================>-------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  37%
[===================================================>----------------------------------------------------------------------------------------]  37%
[====================================================>---------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  40%
[=======================================================>------------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  42%
[==========================================================>---------------------------------------------------------------------------------]  42%
[===========================================================>--------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  45%
[==============================================================>-----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  47%
[=================================================================>--------------------------------------------------------------------------]  47%
[==================================================================>-------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  50%
[=====================================================================>----------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  52%
[========================================================================>-------------------------------------------------------------------]  52%
[=========================================================================>------------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  55%
[============================================================================>---------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  57%
[===============================================================================>------------------------------------------------------------]  57%
[================================================================================>-----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  60%
[===================================================================================>--------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  62%
[======================================================================================>-----------------------------------------------------]  62%
[=======================================================================================>----------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  65%
[==========================================================================================>-------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  67%
[=============================================================================================>----------------------------------------------]  67%
[==============================================================================================>---------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  70%
[=================================================================================================>------------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  72%
[====================================================================================================>---------------------------------------]  72%
[=====================================================================================================>--------------------------------------]  73%
[======================================================================================================>-------------------------------------]  73%
[======================================================================================================>-------------------------------------]  74%
[=======================================================================================================>------------------------------------]  74%
[=======================================================================================================>------------------------------------]  75%
[========================================================================================================>-----------------------------------]  75%
[=========================================================================================================>----------------------------------]  75%
[=========================================================================================================>----------------------------------]  76%
[==========================================================================================================>---------------------------------]  76%
[==========================================================================================================>---------------------------------]  77%
[===========================================================================================================>--------------------------------]  77%
[============================================================================================================>-------------------------------]  78%
[=============================================================================================================>------------------------------]  78%
[=============================================================================================================>------------------------------]  79%
[==============================================================================================================>-----------------------------]  79%
[==============================================================================================================>-----------------------------]  80%
[===============================================================================================================>----------------------------]  80%
[================================================================================================================>---------------------------]  80%
[================================================================================================================>---------------------------]  81%
[=================================================================================================================>--------------------------]  81%
[=================================================================================================================>--------------------------]  82%
[==================================================================================================================>-------------------------]  82%
[===================================================================================================================>------------------------]  83%
[====================================================================================================================>-----------------------]  83%
[====================================================================================================================>-----------------------]  84%
[=====================================================================================================================>----------------------]  84%
[=====================================================================================================================>----------------------]  85%
[======================================================================================================================>---------------------]  85%
[=======================================================================================================================>--------------------]  85%
[=======================================================================================================================>--------------------]  86%
[========================================================================================================================>-------------------]  86%
[========================================================================================================================>-------------------]  87%
[=========================================================================================================================>------------------]  87%
[==========================================================================================================================>-----------------]  88%
[===========================================================================================================================>----------------]  88%
[===========================================================================================================================>----------------]  89%
[============================================================================================================================>---------------]  89%
[============================================================================================================================>---------------]  90%
[=============================================================================================================================>--------------]  90%
[==============================================================================================================================>-------------]  90%
[==============================================================================================================================>-------------]  91%
[===============================================================================================================================>------------]  91%
[===============================================================================================================================>------------]  92%
[================================================================================================================================>-----------]  92%
[=================================================================================================================================>----------]  93%
[==================================================================================================================================>---------]  93%
[==================================================================================================================================>---------]  94%
[===================================================================================================================================>--------]  94%
[===================================================================================================================================>--------]  95%
[====================================================================================================================================>-------]  95%
[=====================================================================================================================================>------]  95%
[=====================================================================================================================================>------]  96%
[======================================================================================================================================>-----]  96%
[======================================================================================================================================>-----]  97%
[=======================================================================================================================================>----]  97%
[========================================================================================================================================>---]  98%
[=========================================================================================================================================>--]  98%
[=========================================================================================================================================>--]  99%
[==========================================================================================================================================>-]  99%
[==========================================================================================================================================>-] 100%
[===========================================================================================================================================>] 100%
[============================================================================================================================================] 100%
                                                                                                                                                   

Running diff_rhyth() on seedlist of size: 10783
NOTE: Using batches in regression.

[>-------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   1%
[=>------------------------------------------------------------------------------------------------------------------------------------------]   2%
[==>-----------------------------------------------------------------------------------------------------------------------------------------]   2%
[===>----------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   3%
[====>---------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   4%
[=====>--------------------------------------------------------------------------------------------------------------------------------------]   5%
[======>-------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   5%
[=======>------------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   6%
[========>-----------------------------------------------------------------------------------------------------------------------------------]   7%
[=========>----------------------------------------------------------------------------------------------------------------------------------]   7%
[==========>---------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   8%
[===========>--------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]   9%
[============>-------------------------------------------------------------------------------------------------------------------------------]  10%
[=============>------------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  10%
[==============>-----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  11%
[===============>----------------------------------------------------------------------------------------------------------------------------]  12%
[================>---------------------------------------------------------------------------------------------------------------------------]  12%
[=================>--------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  13%
[==================>-------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  14%
[===================>------------------------------------------------------------------------------------------------------------------------]  15%
[====================>-----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  15%
[=====================>----------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  16%
[======================>---------------------------------------------------------------------------------------------------------------------]  17%
[=======================>--------------------------------------------------------------------------------------------------------------------]  17%
[========================>-------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  18%
[=========================>------------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  19%
[==========================>-----------------------------------------------------------------------------------------------------------------]  20%
[===========================>----------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  20%
[============================>---------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  21%
[=============================>--------------------------------------------------------------------------------------------------------------]  22%
[==============================>-------------------------------------------------------------------------------------------------------------]  22%
[===============================>------------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  23%
[================================>-----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  24%
[=================================>----------------------------------------------------------------------------------------------------------]  25%
[==================================>---------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  25%
[===================================>--------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  26%
[====================================>-------------------------------------------------------------------------------------------------------]  27%
[=====================================>------------------------------------------------------------------------------------------------------]  27%
[======================================>-----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  28%
[=======================================>----------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  29%
[========================================>---------------------------------------------------------------------------------------------------]  30%
[=========================================>--------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  30%
[==========================================>-------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  31%
[===========================================>------------------------------------------------------------------------------------------------]  32%
[============================================>-----------------------------------------------------------------------------------------------]  32%
[=============================================>----------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  33%
[==============================================>---------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  34%
[===============================================>--------------------------------------------------------------------------------------------]  35%
[================================================>-------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  35%
[=================================================>------------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  36%
[==================================================>-----------------------------------------------------------------------------------------]  37%
[===================================================>----------------------------------------------------------------------------------------]  37%
[====================================================>---------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  38%
[=====================================================>--------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  39%
[======================================================>-------------------------------------------------------------------------------------]  40%
[=======================================================>------------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  40%
[========================================================>-----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  41%
[=========================================================>----------------------------------------------------------------------------------]  42%
[==========================================================>---------------------------------------------------------------------------------]  42%
[===========================================================>--------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  43%
[============================================================>-------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  44%
[=============================================================>------------------------------------------------------------------------------]  45%
[==============================================================>-----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  45%
[===============================================================>----------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  46%
[================================================================>---------------------------------------------------------------------------]  47%
[=================================================================>--------------------------------------------------------------------------]  47%
[==================================================================>-------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  48%
[===================================================================>------------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  49%
[====================================================================>-----------------------------------------------------------------------]  50%
[=====================================================================>----------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  50%
[======================================================================>---------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  51%
[=======================================================================>--------------------------------------------------------------------]  52%
[========================================================================>-------------------------------------------------------------------]  52%
[=========================================================================>------------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  53%
[==========================================================================>-----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  54%
[===========================================================================>----------------------------------------------------------------]  55%
[============================================================================>---------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  55%
[=============================================================================>--------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  56%
[==============================================================================>-------------------------------------------------------------]  57%
[===============================================================================>------------------------------------------------------------]  57%
[================================================================================>-----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  58%
[=================================================================================>----------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  59%
[==================================================================================>---------------------------------------------------------]  60%
[===================================================================================>--------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  60%
[====================================================================================>-------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  61%
[=====================================================================================>------------------------------------------------------]  62%
[======================================================================================>-----------------------------------------------------]  62%
[=======================================================================================>----------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  63%
[========================================================================================>---------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  64%
[=========================================================================================>--------------------------------------------------]  65%
[==========================================================================================>-------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  65%
[===========================================================================================>------------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  66%
[============================================================================================>-----------------------------------------------]  67%
[=============================================================================================>----------------------------------------------]  67%
[==============================================================================================>---------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  68%
[===============================================================================================>--------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  69%
[================================================================================================>-------------------------------------------]  70%
[=================================================================================================>------------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  70%
[==================================================================================================>-----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  71%
[===================================================================================================>----------------------------------------]  72%
[====================================================================================================>---------------------------------------]  72%
[=====================================================================================================>--------------------------------------]  73%
[======================================================================================================>-------------------------------------]  73%
[======================================================================================================>-------------------------------------]  74%
[=======================================================================================================>------------------------------------]  74%
[=======================================================================================================>------------------------------------]  75%
[========================================================================================================>-----------------------------------]  75%
[=========================================================================================================>----------------------------------]  75%
[=========================================================================================================>----------------------------------]  76%
[==========================================================================================================>---------------------------------]  76%
[==========================================================================================================>---------------------------------]  77%
[===========================================================================================================>--------------------------------]  77%
[============================================================================================================>-------------------------------]  78%
[=============================================================================================================>------------------------------]  78%
[=============================================================================================================>------------------------------]  79%
[==============================================================================================================>-----------------------------]  79%
[==============================================================================================================>-----------------------------]  80%
[===============================================================================================================>----------------------------]  80%
[================================================================================================================>---------------------------]  80%
[================================================================================================================>---------------------------]  81%
[=================================================================================================================>--------------------------]  81%
[=================================================================================================================>--------------------------]  82%
[==================================================================================================================>-------------------------]  82%
[===================================================================================================================>------------------------]  83%
[====================================================================================================================>-----------------------]  83%
[====================================================================================================================>-----------------------]  84%
[=====================================================================================================================>----------------------]  84%
[=====================================================================================================================>----------------------]  85%
[======================================================================================================================>---------------------]  85%
[=======================================================================================================================>--------------------]  85%
[=======================================================================================================================>--------------------]  86%
[========================================================================================================================>-------------------]  86%
[========================================================================================================================>-------------------]  87%
[=========================================================================================================================>------------------]  87%
[==========================================================================================================================>-----------------]  88%
[===========================================================================================================================>----------------]  88%
[===========================================================================================================================>----------------]  89%
[============================================================================================================================>---------------]  89%
[============================================================================================================================>---------------]  90%
[=============================================================================================================================>--------------]  90%
[==============================================================================================================================>-------------]  90%
[==============================================================================================================================>-------------]  91%
[===============================================================================================================================>------------]  91%
[===============================================================================================================================>------------]  92%
[================================================================================================================================>-----------]  92%
[=================================================================================================================================>----------]  93%
[==================================================================================================================================>---------]  93%
[==================================================================================================================================>---------]  94%
[===================================================================================================================================>--------]  94%
[===================================================================================================================================>--------]  95%
[====================================================================================================================================>-------]  95%
[=====================================================================================================================================>------]  95%
[=====================================================================================================================================>------]  96%
[======================================================================================================================================>-----]  96%
[======================================================================================================================================>-----]  97%
[=======================================================================================================================================>----]  97%
[========================================================================================================================================>---]  98%
[=========================================================================================================================================>--]  98%
[=========================================================================================================================================>--]  99%
[==========================================================================================================================================>-]  99%
[==========================================================================================================================================>-] 100%
[===========================================================================================================================================>] 100%
[============================================================================================================================================] 100%
                                                                                                                                                   

Plotting

With custom regression, I have to remake clock face plots, genes plots, etc.

setwd(path_to_cyclops_ordering)
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
if (!(dir.exists("downstream_output/plots"))){
  dir.create("downstream_output/plots")
}

#for cycling_in_CTL.csv
plot_clock_face(paste0(path_to_cyclops_ordering, "/downstream_output/plots/CTL_clock_face_plot.png"),"downstream_output/cosinor_results_CTL.csv", mouse_data = mouse_data, BHQ_cutoff = isCyclingBHQCutoff, amp_ratio_cutoff = 0)
[1] "ARNTL set to 0 radians"
NULL
setwd(path_to_cyclops_ordering)

#for cycling_in_AD.csv
plot_clock_face(paste0(path_to_cyclops_ordering, "/downstream_output/plots/AD_clock_face_plot.png"),"downstream_output/cosinor_results_AD.csv",mouse_data = mouse_data, BHQ_cutoff = isCyclingBHQCutoff, amp_ratio_cutoff = 0)
[1] "ARNTL set to 0 radians"
NULL
#plot cyclops histogram
plot_subject_histogram(path_to_cyclops_ordering, "cond_0")
null device 
          1 
plot_subject_histogram(path_to_cyclops_ordering, "cond_1")
null device 
          1 
#Gene Tracings
plot_core_clock_genes(path_to_tmm_file, path_to_cyclops_ordering, useBatch = useBatch, percentile = percentile, split_cond_plots = T)
[1] "NOTE: Using batches in plotting"

Plot Other Genes

plot_me = c("RPL18","RPS7","RPL22","RPS18","RPL8","RPL10A","RPS13","RPL14","RPS15A","RPS12","RPL36AL","RPL34","RPL30","RPL9","RPL21","RPS28","RPSA","RPL26","RPL27A","FAU","RPS3A","RPL7A","RPL17","RPS27A","RPS16","RPL15","RPLP1","RPL7","RPL10","RPL23A","RPL18A","RPL3","RPL12","RPL39","RPL37A","RPL37","RPS10","RPL13","RPL35A","RPS23","RPL13A","RPL38","RPS29","RPL24","RPL41","RPL35","RPS26","RPS2","RPS9","RPL32","RPL6","RPS21","RPS24","RPS25","RPL36","RPL19","RPS27","RPL29","RPS15","RPS3","RPS5","RPS8","RPL27","RSL24D1","RPS6","RPL11")

tmm = read_csv(path_to_tmm_file, show_col_types = FALSE)
  cyc_pred_file = list.files(path = paste0(path_to_cyclops_ordering, "/Fits/"), pattern = '*Fit_Output_*')
cyc_pred = read_csv(paste(path_to_cyclops_ordering, "Fits", cyc_pred_file[1], sep = '/'), show_col_types = FALSE)
plot_gene_trace(cyc_pred, tmm, plot_me , percentile = percentile, useBatch = useBatch)
[1] "NOTE: Using batches in plotting"

EnrichR

Call EnrichR API with python, supplying various lists from cycling and differential rhythm analysis.

path = getwd()
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)
#create list of filenames from the enrichR_files subfolder
gene_lists = list.files("./enrichR_files/", pattern = "^(CTL_|AD_|diff_mesor)")

#run system command to call python script that uses enrichR API
sapply(gene_lists, function(x){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"enrichR_files/EnrichR_background.csv\""))})
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/AD_CTL_mthd2_cyclers_AR25BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/AD_CTL_mthd2_cyclers_AR25BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 4337):
           Ensembl Gene_Symbols
0  ENSG00000244405         ETV5
1  ENSG00000132326         PER2
2  ENSG00000171314        PGAM1
3  ENSG00000188766       SPRED3
4  ENSG00000100335        MIEF1
Background DataFrame (nrow: 13310):
           Ensembl Gene_Symbols
0  ENSG00000188976        NOC2L
1  ENSG00000187961       KLHL17
2  ENSG00000188290         HES4
3  ENSG00000187608        ISG15
4  ENSG00000188157         AGRN
Directory "EnrichR_results/EnrichR_ADCTLmthd2cyclersAR25BHQ1_BCKGRND-EnrichRbackground" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/AD_cyclers_AR25BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/AD_cyclers_AR25BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 3793):
           Ensembl Gene_Symbols
0  ENSG00000244405         ETV5
1  ENSG00000132326         PER2
2  ENSG00000171314        PGAM1
3  ENSG00000130540      SULT4A1
4  ENSG00000115310         RTN4
Background DataFrame (nrow: 13310):
           Ensembl Gene_Symbols
0  ENSG00000188976        NOC2L
1  ENSG00000187961       KLHL17
2  ENSG00000188290         HES4
3  ENSG00000187608        ISG15
4  ENSG00000188157         AGRN
Directory "EnrichR_results/EnrichR_ADcyclersAR25BHQ1_BCKGRND-EnrichRbackground" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/AD_cyclers_AR33BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/AD_cyclers_AR33BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 2036):
           Ensembl Gene_Symbols
0  ENSG00000244405         ETV5
1  ENSG00000132326         PER2
2  ENSG00000171314        PGAM1
3  ENSG00000130540      SULT4A1
4  ENSG00000115310         RTN4
Background DataFrame (nrow: 13310):
           Ensembl Gene_Symbols
0  ENSG00000188976        NOC2L
1  ENSG00000187961       KLHL17
2  ENSG00000188290         HES4
3  ENSG00000187608        ISG15
4  ENSG00000188157         AGRN
Directory "EnrichR_results/EnrichR_ADcyclersAR33BHQ1_BCKGRND-EnrichRbackground" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/CTL_cyclers_AR25BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/CTL_cyclers_AR25BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 3501):
           Ensembl Gene_Symbols
0  ENSG00000244405         ETV5
1  ENSG00000132326         PER2
2  ENSG00000188766       SPRED3
3  ENSG00000171314        PGAM1
4  ENSG00000124785         NRN1
Background DataFrame (nrow: 13310):
           Ensembl Gene_Symbols
0  ENSG00000188976        NOC2L
1  ENSG00000187961       KLHL17
2  ENSG00000188290         HES4
3  ENSG00000187608        ISG15
4  ENSG00000188157         AGRN
Directory "EnrichR_results/EnrichR_CTLcyclersAR25BHQ1_BCKGRND-EnrichRbackground" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/CTL_cyclers_AR33BHQ1.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/CTL_cyclers_AR33BHQ1.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 1678):
           Ensembl Gene_Symbols
0  ENSG00000244405         ETV5
1  ENSG00000132326         PER2
2  ENSG00000188766       SPRED3
3  ENSG00000171314        PGAM1
4  ENSG00000124785         NRN1
Background DataFrame (nrow: 13310):
           Ensembl Gene_Symbols
0  ENSG00000188976        NOC2L
1  ENSG00000187961       KLHL17
2  ENSG00000188290         HES4
3  ENSG00000187608        ISG15
4  ENSG00000188157         AGRN
Directory "EnrichR_results/EnrichR_CTLcyclersAR33BHQ1_BCKGRND-EnrichRbackground" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/diff_mesor_all_genes_BHQ05.csv', 'background_list_file': 'enrichR_files/EnrichR_background.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/diff_mesor_all_genes_BHQ05.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/EnrichR_background.csv
Background DataFrame (nrow: 6464):
           Ensembl Gene_Symbols
0  ENSG00000188976        NOC2L
1  ENSG00000187961       KLHL17
2  ENSG00000188290         HES4
3  ENSG00000187608        ISG15
4  ENSG00000078808         SDF4
Background DataFrame (nrow: 13310):
           Ensembl Gene_Symbols
0  ENSG00000188976        NOC2L
1  ENSG00000187961       KLHL17
2  ENSG00000188290         HES4
3  ENSG00000187608        ISG15
4  ENSG00000188157         AGRN
Directory "EnrichR_results/EnrichR_diffmesorallgenesBHQ05_BCKGRND-EnrichRbackground" already exists. Skipping.
AD_CTL_mthd2_cyclers_AR25BHQ1.csv           AD_cyclers_AR25BHQ1.csv           AD_cyclers_AR33BHQ1.csv          CTL_cyclers_AR25BHQ1.csv 
                                0                                 0                                 0                                 0 
         CTL_cyclers_AR33BHQ1.csv    diff_mesor_all_genes_BHQ05.csv 
                                0                                 0 
isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

setwd("enrichR_files/")
all_DR_gene_lists = list.files( pattern = "^(DR_)")
method2_files = grepl("mthd2", all_DR_gene_lists)
DR_gene_lists_method1 = all_DR_gene_lists[!method2_files]
DR_backgrounds_method1 = paste0("diff_rhythms_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method1, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists_method2 = all_DR_gene_lists[method2_files]
DR_backgrounds_method2 = paste0("diff_rhythms_method2_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method2, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists = c(DR_gene_lists_method1, DR_gene_lists_method2)
DR_backgrounds = c(DR_backgrounds_method1, DR_backgrounds_method2)

# repeat with differential gene lists
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
mapply(function(x, y){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"",y , "\""))},
  DR_gene_lists, 
  DR_backgrounds)
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 54):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000161281       COX7A1  ...  0.020616            -0.704488
1  ENSG00000211450      SELENOH  ...  0.068573            -0.454206
2  ENSG00000164405        UQCRQ  ...  1.000000            -0.565959
3  ENSG00000019582         CD74  ...  1.000000             1.234542
4  ENSG00000177556        ATOX1  ...  1.000000            -0.541007

[5 rows x 10 columns]
Background DataFrame (nrow: 10528):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188976        NOC2L  0.418157  ...  0.787534   1.0             0.333543
1  ENSG00000187961       KLHL17  0.021538  ...  0.402040   1.0             0.371275
2  ENSG00000188290         HES4  0.509391  ...  0.824935   1.0            -0.120408
3  ENSG00000187608        ISG15  0.508770  ...  0.824906   1.0            -0.294342
4  ENSG00000131591     C1orf159  0.782443  ...  0.930163   1.0             0.084900

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio1" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 230):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000161281       COX7A1  ...  0.008463            -0.704488
1  ENSG00000211450      SELENOH  ...  0.028151            -0.454206
2  ENSG00000164405        UQCRQ  ...  0.441316            -0.565959
3  ENSG00000019582         CD74  ...  0.580904             1.234542
4  ENSG00000177556        ATOX1  ...  0.633190            -0.541007

[5 rows x 10 columns]
Background DataFrame (nrow: 4322):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188290         HES4  0.509391  ...  0.772823   1.0            -0.120408
1  ENSG00000187608        ISG15  0.508770  ...  0.772823   1.0            -0.294342
2  ENSG00000131591     C1orf159  0.782443  ...  0.906011   1.0             0.084900
3  ENSG00000176022      B3GALT6  0.360561  ...  0.690359   1.0            -0.083917
4  ENSG00000169972        PUSL1  0.216335  ...  0.599048   1.0            -0.298418

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_CyclingBHQ1AR33_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio33.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_CyclingBHQ1AR33_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio33.csv
Background DataFrame (nrow: 316):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000161281       COX7A1  ...  0.004578            -0.704488
1  ENSG00000211450      SELENOH  ...  0.015228            -0.454206
2  ENSG00000164405        UQCRQ  ...  0.238731            -0.565959
3  ENSG00000124614        RPS10  ...  0.260744            -0.525353
4  ENSG00000137168        PPIL1  ...  0.216483            -0.628644

[5 rows x 10 columns]
Background DataFrame (nrow: 2338):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188290         HES4  0.509391  ...  0.732026   1.0            -0.120408
1  ENSG00000176022      B3GALT6  0.360561  ...  0.629568   1.0            -0.083917
2  ENSG00000175756     AURKAIP1  0.016927  ...  0.155197   1.0            -0.334959
3  ENSG00000235098      ANKRD65  0.025834  ...  0.195471   1.0            -0.320663
4  ENSG00000160075        SSU72  0.160727  ...  0.451659   1.0             0.010688

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersCyclingBHQ1AR33DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio33" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 9):
           Ensembl Gene_Symbols
0  ENSG00000143303       RRNAD1
1  ENSG00000162843        WDR64
2  ENSG00000226479     TMEM185B
3  ENSG00000019582         CD74
4  ENSG00000196422      PPP1R26
Background DataFrame (nrow: 10528):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188976        NOC2L  0.418157  ...  0.787534   1.0             0.333543
1  ENSG00000187961       KLHL17  0.021538  ...  0.402040   1.0             0.371275
2  ENSG00000188290         HES4  0.509391  ...  0.824935   1.0            -0.120408
3  ENSG00000187608        ISG15  0.508770  ...  0.824906   1.0            -0.294342
4  ENSG00000131591     C1orf159  0.782443  ...  0.930163   1.0             0.084900

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRgainAmpADCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio1" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 46):
           Ensembl Gene_Symbols
0  ENSG00000133063        CHIT1
1  ENSG00000162843        WDR64
2  ENSG00000226479     TMEM185B
3  ENSG00000144395      CCDC150
4  ENSG00000114779      ABHD14B
Background DataFrame (nrow: 4322):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188290         HES4  0.509391  ...  0.772823   1.0            -0.120408
1  ENSG00000187608        ISG15  0.508770  ...  0.772823   1.0            -0.294342
2  ENSG00000131591     C1orf159  0.782443  ...  0.906011   1.0             0.084900
3  ENSG00000176022      B3GALT6  0.360561  ...  0.690359   1.0            -0.083917
4  ENSG00000169972        PUSL1  0.216335  ...  0.599048   1.0            -0.298418

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRgainAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_gainAmpAD_CyclingBHQ1AR33_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio33.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_gainAmpAD_CyclingBHQ1AR33_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio33.csv
Background DataFrame (nrow: 62):
           Ensembl Gene_Symbols
0  ENSG00000222046       DCDC2B
1  ENSG00000228063   LYPLAL1-DT
2  ENSG00000162843        WDR64
3  ENSG00000171848         RRM2
4  ENSG00000226479     TMEM185B
Background DataFrame (nrow: 2338):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188290         HES4  0.509391  ...  0.732026   1.0            -0.120408
1  ENSG00000176022      B3GALT6  0.360561  ...  0.629568   1.0            -0.083917
2  ENSG00000175756     AURKAIP1  0.016927  ...  0.155197   1.0            -0.334959
3  ENSG00000235098      ANKRD65  0.025834  ...  0.195471   1.0            -0.320663
4  ENSG00000160075        SSU72  0.160727  ...  0.451659   1.0             0.010688

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRgainAmpADCyclingBHQ1AR33DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio33" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 45):
           Ensembl Gene_Symbols
0  ENSG00000178796       RIIAD1
1  ENSG00000177954        RPS27
2  ENSG00000188010        MORN2
3  ENSG00000143947       RPS27A
4  ENSG00000135617       PRADC1
Background DataFrame (nrow: 10528):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188976        NOC2L  0.418157  ...  0.787534   1.0             0.333543
1  ENSG00000187961       KLHL17  0.021538  ...  0.402040   1.0             0.371275
2  ENSG00000188290         HES4  0.509391  ...  0.824935   1.0            -0.120408
3  ENSG00000187608        ISG15  0.508770  ...  0.824906   1.0            -0.294342
4  ENSG00000131591     C1orf159  0.782443  ...  0.930163   1.0             0.084900

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRlostAmpADCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio1" created.
Saved KEGG_2021_Human results to file
Saved GO_Biological_Process_2023 results to file
Saved MSigDB_Hallmark_2020 results to file
Saved WikiPathway_2021_Human results to file
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 184):
           Ensembl Gene_Symbols
0  ENSG00000142676        RPL11
1  ENSG00000130770      ATP5IF1
2  ENSG00000142937         RPS8
3  ENSG00000173846         PLK3
4  ENSG00000173660        UQCRH
Background DataFrame (nrow: 4322):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188290         HES4  0.509391  ...  0.772823   1.0            -0.120408
1  ENSG00000187608        ISG15  0.508770  ...  0.772823   1.0            -0.294342
2  ENSG00000131591     C1orf159  0.782443  ...  0.906011   1.0             0.084900
3  ENSG00000176022      B3GALT6  0.360561  ...  0.690359   1.0            -0.083917
4  ENSG00000169972        PUSL1  0.216335  ...  0.599048   1.0            -0.298418

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRlostAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio25" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_lostAmpAD_CyclingBHQ1AR33_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_CyclingBHQ1AmpRatio33.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_lostAmpAD_CyclingBHQ1AR33_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_CyclingBHQ1AmpRatio33.csv
Background DataFrame (nrow: 254):
           Ensembl Gene_Symbols
0  ENSG00000175756     AURKAIP1
1  ENSG00000235098      ANKRD65
2  ENSG00000116251        RPL22
3  ENSG00000116288        PARK7
4  ENSG00000142676        RPL11
Background DataFrame (nrow: 2338):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188290         HES4  0.509391  ...  0.732026   1.0            -0.120408
1  ENSG00000176022      B3GALT6  0.360561  ...  0.629568   1.0            -0.083917
2  ENSG00000175756     AURKAIP1  0.016927  ...  0.155197   1.0            -0.334959
3  ENSG00000235098      ANKRD65  0.025834  ...  0.195471   1.0            -0.320663
4  ENSG00000160075        SSU72  0.160727  ...  0.451659   1.0             0.010688

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRlostAmpADCyclingBHQ1AR33DRBHQ2_BCKGRND-diffrhythmsCyclingBHQ1AmpRatio33" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_mthd2_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_mthd2_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 54):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000161281       COX7A1  ...  0.020637            -0.704488
1  ENSG00000211450      SELENOH  ...  0.068645            -0.454206
2  ENSG00000164405        UQCRQ  ...  1.000000            -0.565959
3  ENSG00000019582         CD74  ...  1.000000             1.234542
4  ENSG00000177556        ATOX1  ...  1.000000            -0.541007

[5 rows x 10 columns]
Background DataFrame (nrow: 10539):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188976        NOC2L  0.418157  ...  0.787375   1.0             0.333543
1  ENSG00000187961       KLHL17  0.021538  ...  0.400331   1.0             0.371275
2  ENSG00000188290         HES4  0.509391  ...  0.824404   1.0            -0.120408
3  ENSG00000187608        ISG15  0.508770  ...  0.824372   1.0            -0.294342
4  ENSG00000131591     C1orf159  0.782443  ...  0.930401   1.0             0.084900

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersmthd2CyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio1" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_cyclers_mthd2_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_cyclers_mthd2_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 229):
           Ensembl Gene_Symbols  ...      Bonf  Log_AD_CTL_ampRatio
0  ENSG00000161281       COX7A1  ...  0.008493            -0.704488
1  ENSG00000211450      SELENOH  ...  0.028249            -0.454206
2  ENSG00000164405        UQCRQ  ...  0.442847            -0.565959
3  ENSG00000019582         CD74  ...  0.582920             1.234542
4  ENSG00000177556        ATOX1  ...  0.635387            -0.541007

[5 rows x 10 columns]
Background DataFrame (nrow: 4337):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188290         HES4  0.509391  ...  0.771174   1.0            -0.120408
1  ENSG00000187608        ISG15  0.508770  ...  0.771174   1.0            -0.294342
2  ENSG00000131591     C1orf159  0.782443  ...  0.904076   1.0             0.084900
3  ENSG00000176022      B3GALT6  0.360561  ...  0.689397   1.0            -0.083917
4  ENSG00000169972        PUSL1  0.216335  ...  0.596316   1.0            -0.298418

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRcyclersmthd2CyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_mthd2_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_mthd2_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 9):
           Ensembl Gene_Symbols
0  ENSG00000143303       RRNAD1
1  ENSG00000162843        WDR64
2  ENSG00000226479     TMEM185B
3  ENSG00000019582         CD74
4  ENSG00000196422      PPP1R26
Background DataFrame (nrow: 10539):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188976        NOC2L  0.418157  ...  0.787375   1.0             0.333543
1  ENSG00000187961       KLHL17  0.021538  ...  0.400331   1.0             0.371275
2  ENSG00000188290         HES4  0.509391  ...  0.824404   1.0            -0.120408
3  ENSG00000187608        ISG15  0.508770  ...  0.824372   1.0            -0.294342
4  ENSG00000131591     C1orf159  0.782443  ...  0.930401   1.0             0.084900

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRmthd2gainAmpADCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio1" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_mthd2_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_mthd2_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 45):
           Ensembl Gene_Symbols
0  ENSG00000133063        CHIT1
1  ENSG00000162843        WDR64
2  ENSG00000226479     TMEM185B
3  ENSG00000144395      CCDC150
4  ENSG00000240891       PLCXD2
Background DataFrame (nrow: 4337):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188290         HES4  0.509391  ...  0.771174   1.0            -0.120408
1  ENSG00000187608        ISG15  0.508770  ...  0.771174   1.0            -0.294342
2  ENSG00000131591     C1orf159  0.782443  ...  0.904076   1.0             0.084900
3  ENSG00000176022      B3GALT6  0.360561  ...  0.689397   1.0            -0.083917
4  ENSG00000169972        PUSL1  0.216335  ...  0.596316   1.0            -0.298418

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRmthd2gainAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_mthd2_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_mthd2_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio1.csv
Background DataFrame (nrow: 45):
           Ensembl Gene_Symbols
0  ENSG00000178796       RIIAD1
1  ENSG00000177954        RPS27
2  ENSG00000188010        MORN2
3  ENSG00000143947       RPS27A
4  ENSG00000135617       PRADC1
Background DataFrame (nrow: 10539):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188976        NOC2L  0.418157  ...  0.787375   1.0             0.333543
1  ENSG00000187961       KLHL17  0.021538  ...  0.400331   1.0             0.371275
2  ENSG00000188290         HES4  0.509391  ...  0.824404   1.0            -0.120408
3  ENSG00000187608        ISG15  0.508770  ...  0.824372   1.0            -0.294342
4  ENSG00000131591     C1orf159  0.782443  ...  0.930401   1.0             0.084900

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRmthd2lostAmpADCyclingBHQ1AR1DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio1" already exists. Skipping.
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/DR_mthd2_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv', 'background_list_file': 'diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/DR_mthd2_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: diff_rhythms_method2_CyclingBHQ1AmpRatio25.csv
Background DataFrame (nrow: 184):
           Ensembl Gene_Symbols
0  ENSG00000142676        RPL11
1  ENSG00000130770      ATP5IF1
2  ENSG00000142937         RPS8
3  ENSG00000173846         PLK3
4  ENSG00000173660        UQCRH
Background DataFrame (nrow: 4337):
           Ensembl Gene_Symbols         p  ...       BHQ  Bonf  Log_AD_CTL_ampRatio
0  ENSG00000188290         HES4  0.509391  ...  0.771174   1.0            -0.120408
1  ENSG00000187608        ISG15  0.508770  ...  0.771174   1.0            -0.294342
2  ENSG00000131591     C1orf159  0.782443  ...  0.904076   1.0             0.084900
3  ENSG00000176022      B3GALT6  0.360561  ...  0.689397   1.0            -0.083917
4  ENSG00000169972        PUSL1  0.216335  ...  0.596316   1.0            -0.298418

[5 rows x 10 columns]
Directory "EnrichR_results/EnrichR_DRmthd2lostAmpADCyclingBHQ1AR25DRBHQ2_BCKGRND-diffrhythmsmethod2CyclingBHQ1AmpRatio25" already exists. Skipping.
         DR_cyclers_CyclingBHQ1AR1_DRBHQ2.csv         DR_cyclers_CyclingBHQ1AR25_DRBHQ2.csv 
                                            0                                             0 
        DR_cyclers_CyclingBHQ1AR33_DRBHQ2.csv        DR_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv 
                                            0                                             0 
      DR_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv       DR_gainAmpAD_CyclingBHQ1AR33_DRBHQ2.csv 
                                            0                                             0 
       DR_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv       DR_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv 
                                            0                                             0 
      DR_lostAmpAD_CyclingBHQ1AR33_DRBHQ2.csv    DR_cyclers_mthd2_CyclingBHQ1AR1_DRBHQ2.csv 
                                            0                                             0 
  DR_cyclers_mthd2_CyclingBHQ1AR25_DRBHQ2.csv  DR_mthd2_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv 
                                            0                                             0 
DR_mthd2_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv  DR_mthd2_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv 
                                            0                                             0 
DR_mthd2_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv 
                                            0 
#AD severity
system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/strong_cogdx_diffs_AR25.csv\" -b \"enrichR_files/AD_cyclers_AR25BHQ05.csv\""))
{'lib': ['KEGG_2021_Human', 'GO_Biological_Process_2023', 'MSigDB_Hallmark_2020', 'WikiPathway_2021_Human', 'TRRUST_Transcription_Factors_2019', 'GO_Cellular_Component_2023', 'TRANSFAC_and_JASPAR_PWMs', 'Transcription_Factor_PPIs', 'TargetScan_microRNA_2017', 'miRTarBase_2017'], 'genes_list_file': 'enrichR_files/strong_cogdx_diffs_AR25.csv', 'background_list_file': 'enrichR_files/AD_cyclers_AR25BHQ05.csv'}
Please select file containing list of genes (Symbols)
Path to genes list: enrichR_files/strong_cogdx_diffs_AR25.csv

Please select file containing list of BACKGROUND genes (Symbols)
Path to Background list: enrichR_files/AD_cyclers_AR25BHQ05.csv
Background DataFrame (nrow: 64):
           Ensembl Gene_Symbols
0  ENSG00000160075        SSU72
1  ENSG00000084623        EIF3I
2  ENSG00000163875        MEAF6
3  ENSG00000162783         IER5
4  ENSG00000162817     C1orf115
File not found.
Traceback (most recent call last):
  File "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/Python_EnrichR_for_AnalysisPipeline.py", line 90, in <module>
    background = list(background_df['Gene_Symbols'])
TypeError: 'NoneType' object is not subscriptable
path = getwd()
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)
#create list of filenames from the enrichR_files subfolder
gene_lists = list.files("./enrichR_files/", pattern = "^(CTL_|AD_|diff_mesor)")

#run system command to call python script that uses enrichR API
sapply(gene_lists, function(x){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"enrichR_files/EnrichR_background.csv\""))})
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
AD_CTL_mthd2_cyclers_AR25BHQ1.csv           AD_cyclers_AR25BHQ1.csv           AD_cyclers_AR33BHQ1.csv          CTL_cyclers_AR25BHQ1.csv 
                                2                                 2                                 2                                 2 
         CTL_cyclers_AR33BHQ1.csv    diff_mesor_all_genes_BHQ05.csv 
                                2                                 2 
isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

setwd("enrichR_files/")
all_DR_gene_lists = list.files( pattern = "^(DR_)")
method2_files = grepl("mthd2", all_DR_gene_lists)
DR_gene_lists_method1 = all_DR_gene_lists[!method2_files]
DR_backgrounds_method1 = paste0("diff_rhythms_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method1, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists_method2 = all_DR_gene_lists[method2_files]
DR_backgrounds_method2 = paste0("diff_rhythms_method2_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method2, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists = c(DR_gene_lists_method1, DR_gene_lists_method2)
DR_backgrounds = c(DR_backgrounds_method1, DR_backgrounds_method2)

# repeat with differential gene lists
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
mapply(function(x, y){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"",y , "\""))},
  DR_gene_lists, 
  DR_backgrounds)
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
python3: can't open file '/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/Python_EnrichR_for_AnalysisPipeline.py': [Errno 2] No such file or directory
         DR_cyclers_CyclingBHQ1AR1_DRBHQ2.csv         DR_cyclers_CyclingBHQ1AR25_DRBHQ2.csv 
                                            2                                             2 
        DR_cyclers_CyclingBHQ1AR33_DRBHQ2.csv        DR_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv 
                                            2                                             2 
      DR_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv       DR_gainAmpAD_CyclingBHQ1AR33_DRBHQ2.csv 
                                            2                                             2 
       DR_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv       DR_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv 
                                            2                                             2 
      DR_lostAmpAD_CyclingBHQ1AR33_DRBHQ2.csv    DR_cyclers_mthd2_CyclingBHQ1AR1_DRBHQ2.csv 
                                            2                                             2 
  DR_cyclers_mthd2_CyclingBHQ1AR25_DRBHQ2.csv  DR_mthd2_gainAmpAD_CyclingBHQ1AR1_DRBHQ2.csv 
                                            2                                             2 
DR_mthd2_gainAmpAD_CyclingBHQ1AR25_DRBHQ2.csv  DR_mthd2_lostAmpAD_CyclingBHQ1AR1_DRBHQ2.csv 
                                            2                                             2 
DR_mthd2_lostAmpAD_CyclingBHQ1AR25_DRBHQ2.csv 
                                            2 

FGSEA

path = getwd()
setwd(path_to_cyclops_ordering)
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
if (!(dir.exists("downstream_output/fGSEA"))){
  dir.create("downstream_output/fGSEA")
  dir.create(paste("downstream_output", "fGSEA", "rnk_files", sep = "/"))
  dir.create(paste("downstream_output" , "fGSEA", "fGSEA_results", sep = "/"))
}

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

#create rnk files
write_rnks(path_to_cyclops_ordering, isCyclingBHQCutoff_str)
[1] "Creating rnk files for fGSEA."
#path of parent folder
setwd(path)

#Pathways, downloaded from MsigDB
pathways <- c(gmtPathways("./MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), gmtPathways("./MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))


gene_remapping_dict = read.delim("./MsigDB_gmts_for_GSEA/Human_Gene_Symbol_with_Remapping_MSigDB.v2023.1.Hs.chip", sep = '\t')

setwd(paste(path_to_cyclops_ordering,"downstream_output", "fGSEA", "rnk_files", sep = "/"))

rnk_files = list.files(pattern = ".rnk")


if(!(dir.exists(paste(path_to_cyclops_ordering, "downstream_output","fGSEA","fGSEA_results", sep = "/")))){
  dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results", sep = "/") )
  dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results", "plots",sep = "/"))
}

run_fgsea(rnk_files, gene_remapping_dict, pathways)
[1] "../fGSEA_results/AD_cyclers_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
Saving 7 x 7 in image
[1] "../fGSEA_results/CTL_cyclers_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results/differential_mesor_all_genes_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio1_Log(AD-CTL)ranked.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio1_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio25_Log(AD-CTL)ranked_method2.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio25_Log(AD-CTL)ranked.csv"
[1] "Used std fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio25_minusLogPRanked_method2.csv"
[1] "Used pos fGSEA score type"
[1] "../fGSEA_results/DRgenesAmpRatio25_minusLogPRanked.csv"
[1] "Used pos fGSEA score type"
                                           AD_cyclers_minusLogPRanked.rnk                                           CTL_cyclers_minusLogPRanked.rnk 
                  "../fGSEA_results/plots/AD_cyclers_minusLogPRanked.png"                  "../fGSEA_results/plots/CTL_cyclers_minusLogPRanked.png" 
                         differential_mesor_all_genes_minusLogPRanked.rnk                                    DRgenesAmpRatio1_Log(AD-CTL)ranked.rnk 
"../fGSEA_results/plots/differential_mesor_all_genes_minusLogPRanked.png"           "../fGSEA_results/plots/DRgenesAmpRatio1_Log(AD-CTL)ranked.png" 
                                     DRgenesAmpRatio1_minusLogPRanked.rnk                           DRgenesAmpRatio25_Log(AD-CTL)ranked_method2.rnk 
            "../fGSEA_results/plots/DRgenesAmpRatio1_minusLogPRanked.png"  "../fGSEA_results/plots/DRgenesAmpRatio25_Log(AD-CTL)ranked_method2.png" 
                                  DRgenesAmpRatio25_Log(AD-CTL)ranked.rnk                             DRgenesAmpRatio25_minusLogPRanked_method2.rnk 
         "../fGSEA_results/plots/DRgenesAmpRatio25_Log(AD-CTL)ranked.png"    "../fGSEA_results/plots/DRgenesAmpRatio25_minusLogPRanked_method2.png" 
                                    DRgenesAmpRatio25_minusLogPRanked.rnk 
           "../fGSEA_results/plots/DRgenesAmpRatio25_minusLogPRanked.png" 

Run fgsea on sleep related pathways from https://doi.org/10.1152/physiolgenomics.00275.2006

Phase Set Enrichment Analysis (PSEA)

path = getwd()
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)

# List of pathways, downloaded from MsigDB, absolute paths
psea_pathways <- c(paste0(getwd(), "/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), paste0(getwd(), "/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))

# make sure no spaces when calling cmd
psea_pathways = gsub(" ", "\\ ", psea_pathways, fixed = TRUE) 

# change dir into PSEA directory
setwd(paste(path_to_cyclops_ordering,"downstream_output", "PSEA_files",sep = "/"))
Warning: The working directory was changed to /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/downstream_output/PSEA_files inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.
#list PSEA input files (generated during cosinor regression/DR step)
psea_files = list.files(pattern = "*.txt")

#Save path to ordering as string for cleaning up call to system
path_to_cyclops_ordering_no_space = gsub(" ", "\\ ", path_to_cyclops_ordering, fixed = TRUE)

#dataframe where rows are arguments to system, I will apply system call across rows
arg_df = expand.grid(psea_files, psea_pathways) %>% 
      mutate(out_dirs = paste(str_extract(string = as.character(Var1),     pattern= ".+(?=\\.txt)"), basename(as.character(Var2)) %>% str_extract(pattern= ".+(?=\\.gmt)")%>% 
      gsub(pattern = "\\.", replacement = ""), sep = "_") )

#apply system call, calling PSEA jar file, using rows of arg_df as arguments
apply(arg_df, 1, function(a){
    system(paste0("java -jar ", path_no_space, "/PSEA_cmd.jar ", 
    paste0(path_to_cyclops_ordering_no_space, 
    "/downstream_output/PSEA_files/", a[[1]]), " ", a[[2]]," ",
    paste0(path_to_cyclops_ordering_no_space,
    "/downstream_output/PSEA_files/", a[[3]]), " 5 10000 pdf"))
        })
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_AD_cyclers_AR25BHQ1.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_AD_cyclers_AR25BHQ1_c2cpkeggv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 1728 items
Successfully loaded 186 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_CTL_cyclers_AR25BHQ1.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_CTL_cyclers_AR25BHQ1_c2cpkeggv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 1673 items
Successfully loaded 186 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_DR_AR25BHQ2_acrodiffs.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_DR_AR25BHQ2_acrodiffs_c2cpkeggv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 516 items
Successfully loaded 186 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_AD_cyclers_AR25BHQ1.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_AD_cyclers_AR25BHQ1_hallv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 1728 items
Successfully loaded 50 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_CTL_cyclers_AR25BHQ1.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_CTL_cyclers_AR25BHQ1_hallv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 1673 items
Successfully loaded 50 items
Absolute Path to gene-acrophase file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_DR_AR25BHQ2_acrodiffs.txt
Absolute Path to gmt file: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/Rscripts/automatic_downstream_analysis/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt
Absolute Path to output folder: /Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit//downstream_output/PSEA_files/PSEA_DR_AR25BHQ2_acrodiffs_hallv20231Hssymbols
Min geneset size: 5
Max permutations: 10000
Using output img format: pdf
Successfully loaded 516 items
Successfully loaded 50 items
[1] 0 0 0 0 0 0

Transcription Factor Analysis

Now I search for transcription factors associated with my various gene lists, i.e, TF’s associated with genes that lose amplitude in AD, etc.

Write KEGG Files

Write Files for Kegg Pathway Diagrams

Metabolon

Proteomics

Make sure you have downloaded syn32835854, syn21266449, and syn51389605. You can download programmatically with python or R synapse client. Make sure you specify the path to those downloads with proteiomics_file_path.

Plot Other Proteins

plot_list = c("BPNT1|O95861", "PPM1B|O75688", "BLVRA|P53004", "HDHD2|Q9H0R4")

proteiomics_file_path = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Proteomics/SynapseDownloads/"
tmt_filename = "2b.unlogged_relative_abundance-ROSMAP610.R1+R2-2xTAMPORcorrected.csv" #syn51389605
# tmt_filename = "3.Regressed(age.sex.PMI-noDxProtect)_cleanDat-7814x610-ROSMAP610_R1+R2(Uniprot2019multiconsensus).csv"

plot_prot(proteiomics_file_path, tmt_filename, path_to_rosmap_clin, path_to_cyclops_ordering, c("RPL10|P27635", "RPL32|P62910", "NDUFB1|O75438"), percentile = percentile)

fGSEA on proteomics

---
title: "Perform Downstream Analysis"
output: html_notebook
editor_options: 
  chunk_output_type: inline
---

This notebook is for performing downstream analysis of CYCLOPS. It includes running cosinor regression and assessing differential rhythmicity (two ways for both), calling the enrichR API via python, using fgsea in R, running PSEA, outputing files for making KEGG map diagrams, etc.

### Load Packages

```{r Load Libraries, include=FALSE}
library(reticulate) #use to find conda env for python
library(tidyverse)
source("./differential_rhyth_generalized.R")
source("./create_rnk_files.R")
source("./fgsea.R")
source("./Mesor_Venn_Diagram.R")
source("./Files_for_Pscan.R")
source("./Make_KEGG_map_files.R")
source("./Check_TF_for_cycling_or_DR.R")
source("./fgsea_plot_for_downstream.R")
source("./plot_clock_face_plots.R")
source("./plot_gene_traces_generalized.R")
source("./order_metabolon.R")
source("./order_proteomics.R")
```

This notebook makes use of python via anaconda. Please make sure you install anaconda to proceed:

```{r}
conda_list()
```

Select your conda environment of choice, in my case, item 2 from list above:

```{r}
conda_list()[[2]][2] %>% 
  use_condaenv(required = TRUE)
print(paste("Using cond env:",conda_list()[[1]][2] ))
```

### Setup

Select the CYCLOPS ordering path and path to data file and path to DEseq2 differential expression results:

```{r}
#path to cyclops ordering
path_to_cyclops_ordering = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/training_output/scROSMAP/cogdx_controls/wAD/ExcitatoryNeurons/TMMs_w_batch/Exc3and5_FiltByEdgeRDefault_fixedipBulkChenZhang_condAndBatchCovs_04ContrVar4EGdefault_noTransferFit/"

#path to normalized counts
path_to_tmm_file = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/human_data/Cyclops_folders/tmms/scROSMAP/cogdx_controls/EdgeR_filt_normed/ExcSubtypes3and5_FiltByExprDefault_TMM.csv"

# optional path to file containing differential expression results
deseq_de_filename = "/Users/henryhollis/Box Sync/Henry_stuff/AD_project/scROSMAP/simple_differential_expr/Exc3_5/Exc3_5_filtByExpr_combatSeq_edgeR_DE_exactTest.csv"

path_to_rosmap_clin = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Meta_data/cleaned_rosmap_meta_cogdxConds.csv"
metabolon_filename = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Metabolon/ROSMAP_Metabolon_HD4_Brain514_assay_data.csv"
metabolon_datakey = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Metabolon/ROSMAP_Metabolon_HD4_Data_Dictionary.csv"

#BHQ corrected p cutoff to be considered cycling in analysis:
isCyclingBHQCutoff = 0.1
percentile = 0.025
useBatch = T
```

### Cosinor Regression and Differential Rhythmicity

Run cosinor regression and differential rhythmicity analysis with custom script and with compareRhythms library. I make use of Ensembl and Entrez IDs so I need the following translation dictionaries:

```{r}
# read in translation dict between gene symbols and other alias
Ensembl_dict = readxl::read_xlsx("scROSMAP_ENSEMBL_dict.xlsx")

#run custom cycling and differential rhythmicity analysis
print("***Running cosinor and differential rhythms analysis***")
run_cycling_and_dr_analysis(path_to_cyclops_ordering, path_to_tmm_file, isCyclingSigCutoff = isCyclingBHQCutoff, percentile = percentile, useBatch = useBatch)
```

### Plotting

With custom regression, I have to remake clock face plots, genes plots, etc.

```{r}
setwd(path_to_cyclops_ordering)
if (!(dir.exists("downstream_output/plots"))){
  dir.create("downstream_output/plots")
}

#for cycling_in_CTL.csv
plot_clock_face(paste0(path_to_cyclops_ordering, "/downstream_output/plots/CTL_clock_face_plot.png"),"downstream_output/cosinor_results_CTL.csv", mouse_data = mouse_data, BHQ_cutoff = isCyclingBHQCutoff, amp_ratio_cutoff = 0)

setwd(path_to_cyclops_ordering)

#for cycling_in_AD.csv
plot_clock_face(paste0(path_to_cyclops_ordering, "/downstream_output/plots/AD_clock_face_plot.png"),"downstream_output/cosinor_results_AD.csv",mouse_data = mouse_data, BHQ_cutoff = isCyclingBHQCutoff, amp_ratio_cutoff = 0)

#plot cyclops histogram
plot_subject_histogram(path_to_cyclops_ordering, "cond_0")
plot_subject_histogram(path_to_cyclops_ordering, "cond_1")

#Gene Tracings
plot_core_clock_genes(path_to_tmm_file, path_to_cyclops_ordering, useBatch = useBatch, percentile = percentile, split_cond_plots = T)
```

Plot Other Genes

```{r}
plot_me = c("RPL18","RPS7","RPL22","RPS18","RPL8","RPL10A","RPS13","RPL14","RPS15A","RPS12","RPL36AL","RPL34","RPL30","RPL9","RPL21","RPS28","RPSA","RPL26","RPL27A","FAU","RPS3A","RPL7A","RPL17","RPS27A","RPS16","RPL15","RPLP1","RPL7","RPL10","RPL23A","RPL18A","RPL3","RPL12","RPL39","RPL37A","RPL37","RPS10","RPL13","RPL35A","RPS23","RPL13A","RPL38","RPS29","RPL24","RPL41","RPL35","RPS26","RPS2","RPS9","RPL32","RPL6","RPS21","RPS24","RPS25","RPL36","RPL19","RPS27","RPL29","RPS15","RPS3","RPS5","RPS8","RPL27","RSL24D1","RPS6","RPL11")

tmm = read_csv(path_to_tmm_file, show_col_types = FALSE)
  cyc_pred_file = list.files(path = paste0(path_to_cyclops_ordering, "/Fits/"), pattern = '*Fit_Output_*')
cyc_pred = read_csv(paste(path_to_cyclops_ordering, "Fits", cyc_pred_file[1], sep = '/'), show_col_types = FALSE)
plot_gene_trace(cyc_pred, tmm, plot_me , percentile = percentile, useBatch = useBatch)
```

### EnrichR

Call EnrichR API with python, supplying various lists from cycling and differential rhythm analysis.

```{r}
path = getwd()
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)
#create list of filenames from the enrichR_files subfolder
gene_lists = list.files("./enrichR_files/", pattern = "^(CTL_|AD_|diff_mesor)")

#run system command to call python script that uses enrichR API
sapply(gene_lists, function(x){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"enrichR_files/EnrichR_background.csv\""))})

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

setwd("enrichR_files/")
all_DR_gene_lists = list.files( pattern = "^(DR_)")
method2_files = grepl("mthd2", all_DR_gene_lists)
DR_gene_lists_method1 = all_DR_gene_lists[!method2_files]
DR_backgrounds_method1 = paste0("diff_rhythms_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method1, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists_method2 = all_DR_gene_lists[method2_files]
DR_backgrounds_method2 = paste0("diff_rhythms_method2_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio", str_replace(str_extract(DR_gene_lists_method2, pattern = "AR\\d+"), "AR", ""), ".csv")
DR_gene_lists = c(DR_gene_lists_method1, DR_gene_lists_method2)
DR_backgrounds = c(DR_backgrounds_method1, DR_backgrounds_method2)

# repeat with differential gene lists
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))
mapply(function(x, y){ 
  system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/" ,x, "\" -b \"",y , "\""))},
  DR_gene_lists, 
  DR_backgrounds)

#AD severity
system(paste0("python3 ", path_no_space, "/Python_EnrichR_for_AnalysisPipeline.py -g \"enrichR_files/strong_cogdx_diffs_AR25.csv\" -b \"enrichR_files/AD_cyclers_AR25BHQ05.csv\""))
```

### FGSEA

```{r}
path = getwd()
setwd(path_to_cyclops_ordering)
if (!(dir.exists("downstream_output/fGSEA"))){
  dir.create("downstream_output/fGSEA")
  dir.create(paste("downstream_output", "fGSEA", "rnk_files", sep = "/"))
  dir.create(paste("downstream_output" , "fGSEA", "fGSEA_results", sep = "/"))
}

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

#create rnk files
write_rnks(path_to_cyclops_ordering, isCyclingBHQCutoff_str)

#path of parent folder
setwd(path)

#Pathways, downloaded from MsigDB
pathways <- c(gmtPathways("./MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), gmtPathways("./MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))


gene_remapping_dict = read.delim("./MsigDB_gmts_for_GSEA/Human_Gene_Symbol_with_Remapping_MSigDB.v2023.1.Hs.chip", sep = '\t')

setwd(paste(path_to_cyclops_ordering,"downstream_output", "fGSEA", "rnk_files", sep = "/"))

rnk_files = list.files(pattern = ".rnk")


if(!(dir.exists(paste(path_to_cyclops_ordering, "downstream_output","fGSEA","fGSEA_results", sep = "/")))){
  dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results", sep = "/") )
  dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results", "plots",sep = "/"))
}

run_fgsea(rnk_files, gene_remapping_dict, pathways)
```

Run fgsea on sleep related pathways from https://doi.org/10.1152/physiolgenomics.00275.2006

```{r}
sleep_wake_pathways = gmtPathways("./MsigDB_gmts_for_GSEA/sleep_wake_pathways_w_all_human_aliases_filtered_to_background_genes.gmt")

if(!(dir.exists(paste(path_to_cyclops_ordering, "downstream_output","fGSEA","fGSEA_results_sleep_wake", sep = "/")))){
    dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results_sleep_wake", sep = "/") )
    dir.create( paste(path_to_cyclops_ordering,"downstream_output", "fGSEA","fGSEA_results_sleep_wake", "plots", sep = "/") )
}
setwd(paste(path_to_cyclops_ordering,"downstream_output", "fGSEA", "rnk_files", sep = "/"))

run_fgsea(rnk_files, gene_remapping_dict, sleep_wake_pathways, dir = "fGSEA_results_sleep_wake", max_size = 10000)
```

### Phase Set Enrichment Analysis (PSEA)

```{r}
path = getwd()
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)

# List of pathways, downloaded from MsigDB, absolute paths
psea_pathways <- c(paste0(getwd(), "/MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), paste0(getwd(), "/MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))

# make sure no spaces when calling cmd
psea_pathways = gsub(" ", "\\ ", psea_pathways, fixed = TRUE) 

# change dir into PSEA directory
setwd(paste(path_to_cyclops_ordering,"downstream_output", "PSEA_files",sep = "/"))

#list PSEA input files (generated during cosinor regression/DR step)
psea_files = list.files(pattern = "*.txt")

#Save path to ordering as string for cleaning up call to system
path_to_cyclops_ordering_no_space = gsub(" ", "\\ ", path_to_cyclops_ordering, fixed = TRUE)

#dataframe where rows are arguments to system, I will apply system call across rows
arg_df = expand.grid(psea_files, psea_pathways) %>% 
      mutate(out_dirs = paste(str_extract(string = as.character(Var1),     pattern= ".+(?=\\.txt)"), basename(as.character(Var2)) %>% str_extract(pattern= ".+(?=\\.gmt)")%>% 
      gsub(pattern = "\\.", replacement = ""), sep = "_") )

#apply system call, calling PSEA jar file, using rows of arg_df as arguments
apply(arg_df, 1, function(a){
    system(paste0("java -jar ", path_no_space, "/PSEA_cmd.jar ", 
    paste0(path_to_cyclops_ordering_no_space, 
    "/downstream_output/PSEA_files/", a[[1]]), " ", a[[2]]," ",
    paste0(path_to_cyclops_ordering_no_space,
    "/downstream_output/PSEA_files/", a[[3]]), " 5 10000 pdf"))
        })
```

### 

### Transcription Factor Analysis

Now I search for transcription factors associated with my various gene lists, i.e, TF's associated with genes that lose amplitude in AD, etc.

```{r}
path = getwd()

#create pscan dir if does not exist:
if(!(dir.exists(paste0(path_to_cyclops_ordering, "downstream_output/pscan")))){
  dir.create(paste0(path_to_cyclops_ordering, "downstream_output/pscan") )
}
setwd(paste0(path_to_cyclops_ordering, "downstream_output"))

#grab gene lists from enrichR files directory
gene_lists = list.files("./enrichR_files/", pattern = "^(CTL_|AD_|DR_)")

#write pscan input
lapply(gene_lists, write_pscan_input)
path_no_space = gsub(" ", "\\ ", path, fixed = TRUE)

setwd("pscan/")
pscan_files = list.files("./pscan_files/", pattern = ".csv$")

sapply(pscan_files, function(x){
  system(paste0("python3 ", path_no_space, "/pscan_requests.py --file pscan_files/" ,x))})

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

if(exists("deseq_de_filename")){
  setwd("pscan_results")
  pscan_result_files = list.files(pattern = ".csv$")
  print("Searching cycling and DR results for pscan TF")
  sapply(pscan_result_files, augment_tf_file, deseq_de_filename, isCyclingBHQCutoff_str)
  setwd(paste0(path_to_cyclops_ordering, "downstream_output/enrichR_results"))
  directories = list.files()
  enrichR_TF_paths <- lapply(directories, function(dir) list.files(dir, full.names = TRUE, recursive = TRUE, pattern = ".*TRANSFACandJASPARPWMs_BCKGRND.*\\.csv|.*TranscriptionFactorPPIs_BCKGRND.*\\.csv"))
  enrichR_TF_paths = flatten(enrichR_TF_paths) %>% paste0("./", .)  
  sapply(enrichR_TF_paths, augment_tf_file, deseq_de_filename,     isCyclingBHQCutoff_str)
  
}
```

### Write KEGG Files

Write Files for Kegg Pathway Diagrams

```{r}
entrez_dict = readxl::read_excel("scROSMAP_ENSEMBL_ENTREZ_dict.xlsx")

setwd(path_to_cyclops_ordering)
isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

if (!(dir.exists("downstream_output/KEGG_map_diagrams"))){
  dir.create("downstream_output/KEGG_map_diagrams")
}
write_kegg_map_files(paste0("downstream_output/diff_rhythms_CyclingBHQ", isCyclingBHQCutoff_str, "AmpRatio25.csv"),"Log_AD_CTL_ampRatio", trans_dict = entrez_dict,BHQ_cutoff = 0.2)

```

### Metabolon

```{r}
if (!(dir.exists(paste0(path_to_cyclops_ordering, "/downstream_output/metabolon")))){
  dir.create(paste0(path_to_cyclops_ordering, "/downstream_output/metabolon"))
}

order_metabolon(metabolon_filename, metabolon_datakey, path_to_rosmap_clin, path_to_cyclops_ordering)
```

### Proteomics

Make sure you have downloaded [**syn32835854**]{.underline}, [**syn21266449**]{.underline}, and [**syn51389605**]{.underline}. You can download programmatically with python or R synapse client. Make sure you specify the path to those downloads with *proteiomics_file_path.*

```{r}
proteiomics_file_path = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Proteomics/SynapseDownloads/"
tmt_filename = "2b.unlogged_relative_abundance-ROSMAP610.R1+R2-2xTAMPORcorrected.csv" #syn51389605
# tmt_filename = "3.Regressed(age.sex.PMI-noDxProtect)_cleanDat-7814x610-ROSMAP610_R1+R2(Uniprot2019multiconsensus).csv"

#make sure you have downloaded syn32835854,  syn21266449, and syn51389605
if (!(dir.exists(paste0(path_to_cyclops_ordering, "/downstream_output/proteomics")))){
  dir.create(paste0(path_to_cyclops_ordering, "/downstream_output/proteomics"))
}

order_prot(proteiomics_file_path, tmt_filename, path_to_rosmap_clin, path_to_cyclops_ordering)
```

Plot Other Proteins

```{r}
plot_list = c("BPNT1|O95861", "PPM1B|O75688", "BLVRA|P53004", "HDHD2|Q9H0R4")

proteiomics_file_path = "~/Box Sync/Henry_stuff/AD_project/scROSMAP/Proteomics/SynapseDownloads/"
tmt_filename = "2b.unlogged_relative_abundance-ROSMAP610.R1+R2-2xTAMPORcorrected.csv" #syn51389605
# tmt_filename = "3.Regressed(age.sex.PMI-noDxProtect)_cleanDat-7814x610-ROSMAP610_R1+R2(Uniprot2019multiconsensus).csv"

plot_prot(proteiomics_file_path, tmt_filename, path_to_rosmap_clin, path_to_cyclops_ordering, c("RPL10|P27635", "RPL32|P62910", "NDUFB1|O75438"), percentile = percentile)
```

fGSEA on proteomics

```{r}
path = getwd()
setwd(path_to_cyclops_ordering)
if (!(dir.exists("downstream_output/proteomics/fGSEA"))){
  dir.create("downstream_output/proteomics/fGSEA")
  dir.create("downstream_output/proteomics/fGSEA/rnk_files")
  dir.create("downstream_output/proteomics/fGSEA/fGSEA_results")
}

isCyclingBHQCutoff_str = str_extract(as.character(isCyclingBHQCutoff), "(?<=\\.)\\d+")

#path of parent folder
setwd(path)

write_prot_rnks(path_to_cyclops_ordering)

#Pathways, downloaded from MsigDB
pathways <- c(gmtPathways("./MsigDB_gmts_for_GSEA/c2.cp.kegg.v2023.1.Hs.symbols.gmt"), gmtPathways("./MsigDB_gmts_for_GSEA/h.all.v2023.1.Hs.symbols.gmt"))


gene_remapping_dict = read.delim("./MsigDB_gmts_for_GSEA/Human_UniProt_IDs_MSigDB.v2023.2.Hs.chip", sep = '\t')

setwd(paste0(path_to_cyclops_ordering,"/downstream_output/proteomics/fGSEA/rnk_files"))

rnk_files = list.files(pattern = ".rnk")

run_fgsea(rnk_files, gene_remapping_dict, pathways)
```
